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SCF complex

The SCF complex, also known as the Skp1–Cullin–F-box complex, is a modular multi-subunit E3 ubiquitin ligase that functions within the ubiquitin-proteasome system to selectively target regulatory proteins for polyubiquitination and subsequent degradation by the 26S proteasome.^[1] This process is critical for controlling diverse cellular functions, including cell cycle progression, DNA replication and repair, signal transduction, and transcriptional regulation, with the SCF representing the largest family of such ligases in eukaryotes.^[2] Discovered in the late 1990s through studies in yeast and mammals, the SCF complex enables precise temporal control of protein levels by recognizing specific substrates, often in a phosphorylation-dependent manner, thereby ensuring genome stability and preventing aberrant cell proliferation.^[3]

Structure and Components

The SCF complex is assembled around a rigid scaffold provided by the Cullin 1 (Cul1) protein, which adopts an elongated α-helical structure approximately 100 Å long, serving as a bridge between substrate-recognition and ubiquitin-transfer modules.^[1] At its N-terminus, Cul1 binds the adaptor protein Skp1, which in turn recruits one of numerous interchangeable F-box proteins that dictate substrate specificity through their F-box domain (an ~40-amino-acid motif) and diverse protein-protein interaction domains, such as WD40 repeats in FBXW proteins or leucine-rich repeats in FBXL proteins.^[2] The C-terminal domain of Cul1 interacts with the small RING finger protein Rbx1 (Roc1), which positions an E2 ubiquitin-conjugating enzyme to facilitate the transfer of ubiquitin moieties from E1-activating enzymes onto lysine residues of the substrate, forming polyubiquitin chains that signal degradation.^[3] In humans, there are 72 F-box proteins (as of 2025), classified into FBXW (11 members, e.g., FBXW7 targeting cyclin E), FBXL (22 members, e.g., Skp2 degrading p27), and FBXO (39 members, e.g., FBXO31 involved in DNA damage response) families, allowing the SCF to address a wide array of substrates.^[2]^[4]

Mechanism and Regulation

Substrate recognition by SCF typically requires prior phosphorylation of the target protein by kinases such as cyclin-dependent kinases (CDKs), creating a binding motif like the Cdc4-phosphodegron (CPD) or KEN-box that is captured by the F-box protein's substrate-binding domain.^[1] Once bound, the proximity of the E2~Ub (ubiquitin-charged E2) to the substrate, enabled by Cul1's scaffold and Rbx1's RING domain, promotes iterative ubiquitination, often yielding K48-linked chains that direct proteasomal destruction.^[3] Activity is further regulated by neddylation, a post-translational modification where the ubiquitin-like protein NEDD8 conjugates to a conserved lysine on Cul1 (Lys720 in humans), enhancing E2 recruitment and ligase efficiency by inducing conformational changes.^[1] Additional regulators include the CAND1 protein, which sequesters Cul1 to inhibit assembly, and deneddylases like CSN5, which promote complex disassembly for recycling; disruptions in these dynamics can lead to substrate accumulation and cellular dysfunction.

Biological and Clinical Significance

SCF complexes are indispensable for eukaryotic development and homeostasis, with roles extending from yeast cell cycle control (e.g., SCF^Cdc4 degrading Sic1 to initiate S phase) to mammalian processes like auxin signaling in plants via SCF^TIR1 and immune responses in animals.^[5] In humans, SCF dysregulation—such as overexpression of Skp2 in cancers leading to p27 depletion and unchecked proliferation, or FBXW7 mutations leading to stabilization of oncoproteins like c-Myc—is strongly linked to tumorigenesis across tissues including breast, ovarian, and colorectal cancers, where it drives chromosomal instability and therapeutic resistance.^[2] For instance, SKP1 deletions occur in up to 44% of ovarian tumors, while β-TrCP variants impair degradation of oncogenic substrates like β-catenin in Wnt pathway-driven malignancies.^[2] These insights have spurred therapeutic interest, with SCF inhibitors (e.g., targeting Skp2 or FBXW7 interfaces) emerging as potential anticancer agents to restore proteostasis and halt tumor progression.^[6]

Structure and Components

Core Components

The SCF complex, a multi-subunit E3 ubiquitin ligase, is anchored by three invariant core components: Skp1, Cullin-1 (CUL1), and RING-box protein 1 (RBX1). These proteins form a rigid scaffold that positions substrate specificity factors and catalytic elements for targeted ubiquitination. Skp1 acts as an adaptor protein, binding directly to the F-box domain of variable F-box proteins to integrate them into the complex. This interaction occurs through a helical region in Skp1 that engages the F-box motif, ensuring modular assembly without altering the core architecture.^[7] CUL1 serves as the elongated structural backbone of the SCF complex, adopting a rod-like conformation approximately 95 Å in length that spatially organizes the other subunits. The N-terminal domain of CUL1 interacts with Skp1 via a conserved helix, while the C-terminal domain binds RBX1, creating a modular platform that holds the adaptor-substrate module distant from the catalytic RING domain.^[7] RBX1, a small RING-finger protein, docks onto the C-terminus of CUL1 and presents its RING domain to recruit E2 ubiquitin-conjugating enzymes, such as UBE2D family members, thereby facilitating ubiquitin transfer.^[8] Crystal structures of the Skp1-CUL1-RBX1 trimer reveal atomic-level details of these interfaces, including hydrogen bonds and hydrophobic contacts that stabilize the complex, with the RBX1 RING domain positioned about 50 Å from the Skp1-binding site to enable efficient catalysis. Activation of the SCF core requires covalent modification of CUL1 by the ubiquitin-like protein NEDD8, a process known as neddylation, which occurs at a specific lysine residue (Lys720 in human CUL1).^[9] Neddylation proceeds through a ubiquitin-like cascade involving the E1-activating enzyme (NAE1/UBA3 heterodimer), the E2-conjugating enzyme UBE2M (also known as UBC12), and occasionally RBX1 acting as a co-E3, resulting in an isopeptide bond between NEDD8's C-terminus and CUL1's lysine side chain.^[10] This modification induces conformational changes in CUL1, enhancing E2 recruitment to the RING domain by up to 100-fold and rigidifying the scaffold to optimize ubiquitin ligation geometry.00942-2) Structural studies confirm that neddylated CUL1 adopts an extended conformation, with NEDD8 binding near the CUL1 C-terminus to stabilize RBX1 positioning.^[11]

F-box Protein Diversity

The SCF complex achieves substrate specificity through its variable F-box protein subunits, which serve as adaptors that link target proteins to the core ubiquitination machinery. In humans, the genome encodes 69 F-box proteins, enabling a wide range of regulatory functions across cellular processes. These proteins are classified into three major subfamilies based on their C-terminal substrate-binding domains: FBXW proteins, which contain WD40 repeats; FBXL proteins, featuring leucine-rich repeats (LRR); and FBXO proteins, which possess diverse or no characterized motifs beyond the F-box domain itself. This classification reflects the modular nature of F-box proteins, where the conserved N-terminal F-box motif mediates binding to Skp1, while the C-terminal domains confer specificity.^[12] Substrate recognition by F-box proteins primarily occurs through their WD40 or LRR domains, which interact with phosphorylated motifs on target proteins, often in a phosphorylation-dependent manner.80330-4) For instance, WD40 repeats in FBXW proteins form β-propeller structures that bind short phosphodegrons, while LRR domains in FBXL proteins create elongated scaffolds for larger substrate interfaces.00450-3) This domain-mediated binding ensures selective recruitment, allowing the SCF complex to target distinct substrates under specific conditions. Prominent examples illustrate this diversity: Skp2 (FBXL1), an FBXL family member, recognizes and promotes the degradation of cell cycle inhibitors like p27^{Kip1} and cyclin E via its LRR domain. β-TrCP (FBXW11), from the FBXW subfamily, targets signaling proteins such as β-catenin and IκBα through its WD40 repeats, regulating pathways like Wnt and NF-κB. Similarly, Fbw7 (FBXW7), another FBXW protein, uses its WD40 domain to bind and ubiquitinate oncoproteins including cyclin E and c-Myc, controlling proliferation.00175-3) F-box protein diversity is evolutionarily conserved across eukaryotes, underscoring their fundamental role in ubiquitin-mediated proteolysis. In the yeast Saccharomyces cerevisiae, approximately 20 F-box proteins have been identified, many of which parallel mammalian counterparts in function and domain architecture. Mutations in F-box genes can disrupt substrate-binding domains, leading to loss of specificity and aberrant SCF activity, as seen in cases where altered WD40 or LRR interfaces fail to discriminate targets properly.^[13]

Discovery and History

Initial Identification in Yeast

The foundational components of the SCF complex were uncovered through genetic screens in the budding yeast Saccharomyces cerevisiae during the early 1990s, focusing on mutants defective in cell cycle progression at the G1/S transition. Cdc53, the yeast ortholog of the cullin family member CUL1, was identified in a screen for high-copy suppressors and genetic interactors of cdc34, an E2 ubiquitin-conjugating enzyme whose mutants exhibit G1/S checkpoint defects characterized by elongated buds and undivided nuclei. Cdc4, an F-box-containing protein serving as the substrate recognition subunit, was originally isolated in earlier cell division cycle (CDC) screens but was further characterized in the 1990s through yeast two-hybrid assays that revealed its interaction with Skp1 via the conserved F-box motif.^[14] Skp1 was discovered simultaneously as a dosage suppressor of cdc4 temperature-sensitive mutants and as a Cdc4-binding protein in two-hybrid screens using human cyclin F as bait, highlighting its role as an adaptor linking F-box proteins to the cullin scaffold.^[14] Genetic interactions among cdc34, cdc4, and cdc53 mutants established their coordinated function in ubiquitin-mediated proteolysis, as double and triple mutants displayed synthetic lethality and shared G1 arrest phenotypes with duplicated spindle pole bodies but undivided nuclei, indicating a common pathway for degrading cell cycle regulators to promote S-phase entry. These findings linked the SCF core to the E2 enzyme Cdc34, which provides ubiquitin-charging activity essential for G1/S progression. In 1997, Sic1 was identified as a key substrate whose multi-site phosphorylation by cyclin-dependent kinases enables its recognition and ubiquitin-dependent degradation by the SCF^{Cdc4} complex, thereby relieving inhibition of S-phase cyclins (Clb5/6-Cdc28) to trigger the Start transition in the cell cycle.^[15] Overexpression of non-phosphorylatable Sic1 blocked DNA replication, underscoring SCF's role in timing this commitment point.^[15] Early biochemical efforts in the mid-1990s purified SCF complexes from yeast extracts using affinity chromatography on epitope-tagged Cdc53 or Cdc4, revealing stable associations among Skp1, Cdc53, Cdc4, Cdc34, and the substrate Sic1, and demonstrating their ubiquitin ligase activity in vitro toward phosphorylated G1 regulators.^[16] These purifications confirmed the modular architecture and provided the first direct evidence of SCF's E3 activity in yeast cell cycle control.

Key Advances in Mammalian Systems

Following the initial discoveries in yeast, significant progress in understanding the SCF complex occurred in mammalian systems during the late 1990s, with the identification of key components linked to cell cycle control. In 1998, human cullin-1 (CUL1) was cloned and demonstrated to form an evolutionarily conserved ubiquitin ligase complex with SKP1 and the F-box protein SKP2, analogous to the yeast SCF, thereby establishing its role in mammalian ubiquitination pathways. This finding was rapidly expanded in 1999 through the identification of a large family of 26 human F-box proteins, including diverse subtypes such as FBXW (WD40-repeat containing) and FBXL (leucine-rich repeat containing), with SKP2 specifically implicated in targeting cell cycle inhibitors for degradation during S-phase entry. These studies highlighted the modular nature of mammalian SCF complexes, where F-box proteins confer substrate specificity, enabling regulation of proliferation in higher eukaryotes. In the 2000s, the SCF architecture was further connected to tumor suppression and disease-relevant pathways, exemplified by investigations into the von Hippel-Lindau (VHL) protein. In 1999, VHL was identified as a substrate-recognition subunit in an E3 ubiquitin ligase complex containing elongin B/C, CUL2, and Rbx1, initially described as SCF-like due to structural and functional similarities, though later clarified as the distinct CRL2^{VHL} complex responsible for hypoxia-inducible factor (HIF) degradation.^[17] This linkage, despite the CRL2 distinction, spurred broader interest in cullin-based ligases and resolved early nomenclature confusion around F-box adaptors in mammalian ubiquitin signaling, influencing studies on renal cell carcinoma and oxygen sensing. Advancing into the 2010s, structural biology breakthroughs, particularly with cryo-electron microscopy (cryo-EM), illuminated the atomic details of full-length SCF assemblies with substrates, surpassing earlier crystal structures of subcomplexes. A pivotal example is the high-resolution cryo-EM structure of the SCF^{Skp2}-Cks1 complex bound to phosphorylated p27^{Kip1} and the CDK2-cyclin A kinase, resolved at 3.4 Å in 2023, which captured dynamic conformations of the hexameric module and revealed how Cks1 allosterically enhances substrate positioning for ubiquitination.^[18] These visualizations underscored the conformational flexibility in mammalian SCF, facilitating precise targeting of cell cycle regulators like p27. Recent studies have deepened insights into SCF regulation through exchange of F-box subunits. A 2023 analysis using cryo-EM reconstructed multiple states of CAND1-bound SCF complexes across F-box variants (e.g., FBXW7, SKP2, FBXO6), demonstrating how CAND1 promotes allosteric disassembly of neddylated SCF for rapid adaptation to changing cellular substrates, with resolution up to 2.7 Å revealing key interfacial contacts.^[19] This work highlights CAND1's role as a chaperone in maintaining SCF diversity and efficiency in mammals, integrating prior biochemical models with structural evidence of regulatory dynamics.

Mechanism of Action

Ubiquitination Process

The ubiquitination process mediated by the SCF (Skp1-Cullin-F-box) complex follows the canonical hierarchical cascade of the ubiquitin-proteasome system, involving sequential enzymatic steps to attach ubiquitin molecules to target proteins. In the initial activation step, ubiquitin is conjugated to an E1-activating enzyme (such as UBA1 in humans) through an ATP-dependent thioester bond formation at the C-terminal glycine of ubiquitin; this reaction hydrolyzes ATP to AMP and pyrophosphate, providing the energy for subsequent transfers.^[20] The activated ubiquitin is then transferred from E1 to an E2-conjugating enzyme, typically Cdc34 in yeast (UBE2R1 in humans, often in cooperation with UBE2D family enzymes for initiation), forming another thioester bond, which positions the ubiquitin for ligation.^[21] As a multi-subunit Cullin-RING E3 ligase, SCF facilitates the final transfer of ubiquitin from the E2 to the ε-amino group of a lysine residue on the substrate protein, with the F-box protein providing substrate specificity through its adaptor role.^[21] SCF promotes processive polyubiquitination, attaching multiple ubiquitin molecules in a single encounter with the substrate to form K48-linked chains, which are recognized by the 26S proteasome for degradation. This processivity contrasts with distributive mechanisms in other E3 ligases and ensures efficient tagging, where the first ubiquitin attachment to the substrate is rate-limiting, followed by rapid elongation of the chain.^[22] The kinetics of chain elongation are accelerated by the acidic loop in Cdc34, which positions the K48 residue of the substrate-linked ubiquitin to attack the SCF-bound Cdc34~ubiquitin thioester, enabling successive additions at rates up to 1-2 ubiquitins per second under optimal conditions.^[22] Unlike some RING E3 ligases that primarily mediate mono-ubiquitination for signaling roles, SCF's architecture supports polyubiquitin chain assembly specifically for proteasomal targeting.^[20] A critical regulatory step in SCF's ubiquitination activity is the neddylation of Cullin-1 (CUL1), the scaffold subunit, which conjugates the ubiquitin-like protein NEDD8 to a conserved lysine (K720 in human CUL1) via a parallel E1-E2-E3 cascade involving NAE1/UBA3 (E1), UBE2M (E2), and RBX1 (E3).^[11] This modification induces a conformational change in CUL1's C-terminal domain, repositioning the RBX1 RING domain and its associated E2~ubiquitin closer to the substrate (within ~40 Å), thereby enhancing ubiquitin transfer efficiency by approximately 5- to 7-fold compared to the unneddylated state.^[11] Structural studies confirm that neddylation rigidifies the complex and aligns the catalytic elements, distinguishing SCF from non-neddylated E3s that rely on alternative activation mechanisms.^[23]

Assembly and Disassembly Dynamics

The assembly and disassembly of the SCF complex are tightly regulated to allow dynamic exchange of F-box proteins, ensuring precise targeting of substrates for ubiquitination. Central to this process is the cullin-RING ligase (CRL) exchange factor CAND1, which binds specifically to the unneddylated form of CUL1, the scaffold protein of SCF, thereby inhibiting premature assembly and facilitating the dissociation of existing F-box–Skp1 modules from the CUL1–RBX1 core. This binding promotes the exchange of F-box subunits, enabling the SCF complex to adapt to changing cellular needs by rapidly equilibrating with diverse F-box proteins. Real-time measurements have shown that CAND1 accelerates the disassembly of SCF complexes, with depletion of CAND1 leading to stabilization of suboptimal F-box associations and altered SCF landscapes in cells.^[24] A key structural insight into this mechanism comes from cryo-electron microscopy studies revealing an allosteric rocking motion of CAND1 around the CUL1 subunit. In this model, CAND1 initially clasps the inactive catalytic domains of the SCF complex, then rolls along the CUL1 surface, inducing conformational changes that destabilize the F-box–Skp1 interaction and promote disassembly. This dynamic "CAND1-SCF conformational ensemble" recycles CUL1 for reassembly into new complexes, preventing the persistence of idle SCF variants. The process ensures substrate fidelity by disassembling non-productive or substrate-depleted SCF complexes, thereby avoiding off-target ubiquitination and maintaining specificity in protein degradation pathways.00213-1)31238-2) Neddylation and deneddylation cycles further govern SCF dynamics, with neddylation activating the complex for ubiquitination and deneddylation enabling disassembly. The E2-like enzyme DCNL1 (also known as DCN1) catalyzes the attachment of the ubiquitin-like protein NEDD8 to a conserved lysine on CUL1, promoting a conformational shift that repositions the RBX1–RING domain for optimal ubiquitin transfer and sterically hindering CAND1 binding. Conversely, the COP9 signalosome (CSN) complex performs deneddylation by hydrolyzing the NEDD8–CUL1 isopeptide bond via its metalloprotease subunit CSN5, returning CUL1 to its unneddylated state and allowing CAND1-mediated exchange. This reciprocal regulation creates an oscillatory cycle: neddylation assembles and activates SCF for substrate engagement, while CSN-mediated deneddylation inactivates it post-activity, facilitating F-box turnover.^[25]00259-8) Recent findings have identified CAND2 as a distinct regulator that operates in parallel to CAND1 for specific SCF variants. Unlike CAND1, which broadly modulates SCF assembly, CAND2 binds unneddylated CUL1 in a manner that enhances degradation of select substrates, acting as an F-box exchange factor tailored to particular cellular contexts such as stress responses. Structural and biochemical analyses reveal that CAND2 induces unique conformational adjustments in CUL1, promoting efficient SCF reassembly for targeted proteolysis while maintaining fidelity in ubiquitin ligase activity. This specialization underscores a layered regulatory network where CAND1 and CAND2 cooperatively fine-tune SCF dynamics.^[26]

Biological Functions

Cell Cycle Regulation

The SCF ubiquitin ligase complex plays a pivotal role in eukaryotic cell cycle progression by targeting key regulatory proteins for proteasomal degradation, ensuring timely transitions between phases. Various SCF complexes target many known cell cycle regulators, highlighting their broad influence on proliferation control.^[27] In yeast, the SCF^Cdc4 complex degrades the cyclin-dependent kinase inhibitor Sic1 upon its multisite phosphorylation by G1 cyclins, thereby activating S-phase cyclins (Clb5/6-Cdc28) to initiate DNA replication and enforce the G1/S checkpoint; this mechanism is homologous to mammalian cyclin-dependent kinase inhibitors (CKIs) like p27^Kip1 and p21^Cip1.^[28] During the G1/S transition, the SCF^Skp2 complex promotes cell cycle entry by ubiquitinating and degrading CKIs that inhibit cyclin E-CDK2 activity. Specifically, phosphorylation of p27^Kip1 at Thr187 by cyclin E-CDK2 enables its recognition by SCF^Skp2, leading to p27 degradation and derepression of CDK2 to drive S-phase progression.^[29] Similarly, SCF^Skp2 targets p21^Cip1 for degradation in a phosphorylation-dependent manner during late G1, further facilitating the activation of CDK2-cyclin E complexes essential for DNA synthesis initiation.^[30] In late G1 and early S phase, SCF^Fbw7 ensures proper timing by degrading hyperphosphorylated cyclin E, preventing excessive CDK2 activity that could lead to replication errors. Cyclin E, initially stabilized to promote G1/S entry, becomes a substrate for SCF^Fbw7 following phosphorylation at multiple sites by CDK2 and GSK3β, resulting in its ubiquitination and clearance as cells progress into S phase.^[31] At the G2/M transition, SCF^βTrCP contributes to mitotic entry by eliminating inhibitors of CDK1. It ubiquitinates Wee1 kinase, a negative regulator of CDK1, after its phosphorylation by PLK1 and CDK1, thereby reducing Wee1 levels to allow CDK1-cyclin B activation and progression into mitosis. Additionally, SCF^βTrCP targets Emi1, an inhibitor of the anaphase-promoting complex/cyclosome (APC/C), for degradation in prophase; this step, triggered by CDK1 and PLK1 phosphorylation of Emi1, relieves APC/C inhibition and supports the accumulation of mitotic cyclins.^[32] SCF complexes also enforce cell cycle checkpoints in response to DNA damage. For instance, SCF^Fbxo31 mediates the degradation of cyclin D1 in a phosphorylation-dependent manner following genotoxic stress, inducing G1 arrest to allow DNA repair; this involves ATM/ATR kinase signaling that activates SCF^Fbxo31 to ubiquitinate cyclin D1 at Thr286.^[33]

Developmental and Signaling Roles

The SCF complex plays a pivotal role in cellular signaling pathways by targeting key regulatory proteins for ubiquitin-mediated degradation, thereby modulating signal transduction and preventing aberrant activation. In the Wnt/β-catenin pathway, SCF^βTrCP recognizes a phosphorylated destruction motif on β-catenin (Ser-33/Ser-37), facilitating its ubiquitination and proteasomal degradation to attenuate canonical Wnt signaling and maintain appropriate levels of β-catenin-dependent transcription.^[34] This mechanism ensures precise control of cell fate decisions influenced by Wnt gradients. Similarly, in the NF-κB pathway, SCF^βTrCP (with its Drosophila homolog Slimb) binds phosphorylated IκBα (Ser-32/Ser-36), promoting its ubiquitination at Lys-21 and Lys-22, which leads to IκBα degradation and subsequent nuclear translocation of NF-κB dimers to activate pro-inflammatory and survival gene expression.^[35] In the Notch signaling pathway, SCF^Fbw7 targets the Notch intracellular domain (NICD) for degradation following its release from the membrane, thereby limiting the duration and intensity of Notch-mediated transcriptional responses that influence cell differentiation and proliferation. Beyond acute signaling, the SCF complex contributes to organismal development by fine-tuning patterning and morphogenesis through pathway crosstalk. In Drosophila embryonic development, SCF^Slimb regulates segment polarity by degrading Armadillo (the β-catenin ortholog) in the absence of Wingless signaling, preventing ectopic activation of Wingless target genes, while also processing Cubitus interruptus (Ci) in the Hedgehog pathway to generate a transcriptional repressor form that restricts Hedgehog-responsive expression.^[36] This dual action of Slimb ensures proper anterior-posterior patterning and denticle belt formation in the larval cuticle. Mammalian homologs, such as βTrCP and Fbw7, extend these roles to vertebrate development; for instance, SCF^βTrCP-mediated β-catenin turnover is essential for limb bud formation and proximal-distal patterning via Wnt signaling in the apical ectodermal ridge, while SCF^Fbw7 degrades NICD to regulate vascular remodeling and somitogenesis during embryogenesis. These processes highlight SCF's conservation in translating signaling inputs into developmental outcomes. Recent studies underscore SCF's involvement in maintaining genomic integrity during cellular differentiation, a process integral to development. SCF complexes, including SCF^βTrCP and SCF^Fbw7, regulate cell cycle effectors like cyclin E and p27 to coordinate DNA replication and chromosome segregation with differentiation cues, preventing aneuploidy and ensuring stable genome transmission in progenitors transitioning to specialized lineages.^[8] For example, SCF^Fbw7-dependent cyclin E degradation facilitates timely S-phase progression in cellular differentiation, linking ubiquitin-mediated proteolysis to epigenetic and morphological changes in developing tissues.^[8]

Role in Disease

Implications in Cancer

Dysregulation of the SCF complex plays a pivotal role in tumorigenesis through aberrant ubiquitination of key regulators, particularly via oncogenic F-box proteins that promote cell proliferation and survival. Overexpression of Skp2, an F-box protein in the SCF^{Skp2} complex, is frequently observed in various human cancers, where it targets the cyclin-dependent kinase inhibitor p27 for proteasomal degradation, thereby unleashing unchecked cell cycle progression and enhancing proliferative capacity.^[37] This overexpression is associated with poor prognosis across multiple cancer types, including breast, prostate, and lung cancers, by destabilizing tumor suppressors and facilitating oncogenic signaling. Mutations in Fbw7, another F-box subunit of the SCF^{Fbw7} complex, are frequent in certain malignancies and lead to stabilization of proto-oncoproteins. In colorectal cancers, Fbw7 mutations occur in 10-15% of cases, impairing the degradation of substrates like c-Myc, which accumulates and drives uncontrolled transcription of genes promoting cell growth and metastasis.^[38] Similarly, βTrCP, as part of SCF^{βTrCP}, contributes to chemoresistance by facilitating NF-κB hyperactivation; elevated βTrCP levels in pancreatic and other cancers stabilize NF-κB components, enhancing survival signals and reducing apoptosis in response to chemotherapeutic agents.^[39] Therapeutic targeting of SCF components has emerged as a promising strategy to restore proteostasis and combat oncoprotein accumulation. A 2024 patent review highlights advances in SCF inhibitors, including small molecules and nucleic acid-based approaches like Skp2 siRNAs, which have shown preclinical efficacy in inducing p27 stabilization and apoptosis in glioblastoma models, with some advancing toward clinical evaluation.^[40] Additionally, proteolysis-targeting chimeras (PROTACs) exploit SCF ligases to selectively degrade oncoproteins; for instance, PROTACs recruiting SCF^{βTrCP} or SCF^{Fbw7} have demonstrated potent antitumor effects by ubiquitinating targets like cyclin E1 or c-Myc in preclinical cancer models, offering a nuanced approach to overcome resistance in proliferative tumors.^[41]

Involvement in Other Pathologies

The SCF complex plays a significant role in antiviral immunity through its F-box proteins, which mediate the ubiquitination and degradation of viral components to restrict infection. A 2025 review highlights that F-box proteins, including those in SCF complexes, recognize and degrade key viral proteins, thereby exerting antiviral effects by disrupting viral replication and modulating host interferon pathways.^[42] For instance, SCF^βTrCP targets the surface protein of hepatitis B virus for proteasomal degradation, limiting viral assembly and propagation in infected hepatocytes.^[43] This mechanism underscores the SCF complex's contribution to innate immune defense against viruses, with dysregulation potentially exacerbating chronic infections. In myelodysplastic syndromes (MDS), the SCF-FBXO11 complex regulates RNA splicing in hematopoietic stem cells, influencing disease progression. A 2023 American Society of Hematology abstract demonstrates that SCF-FBXO11 ubiquitinates and degrades a network of RNA-binding proteins, thereby controlling alternative splicing events critical for erythroid differentiation and cell survival under stress.^[44] Loss-of-function in FBXO11, observed in MDS patients, leads to dysregulated splicing of genes involved in cytokine signaling and apoptosis, promoting ineffective hematopoiesis and clonal expansion of aberrant stem cells. This pathway highlights SCF-FBXO11 as a potential therapeutic target for splicing-related defects in MDS. In cardiovascular pathologies, SCF complexes drive vascular smooth muscle cell (VSMC) proliferation, a key event in atherosclerosis. SCF^Skp2 promotes VSMC growth by targeting cyclin-dependent kinase inhibitors for degradation, leading to neointima formation and plaque instability.^[45] Experimental models demonstrate that Skp2 overexpression in hyperlipidemic mice accelerates intimal thickening and foam cell accumulation, while inhibition attenuates lesion progression. This proliferative role positions SCF^Skp2 as a contributor to chronic vascular remodeling in atherosclerosis. The SCF-Fbxo11 complex also influences T-cell regulation, modulating antigen presentation and immune tolerance. FBXO11 negatively regulates MHC class II expression by ubiquitinating the transcription factor CIITA, thereby suppressing CD4^+ T-cell activation.^[46] Mutations or loss of FBXO11 lead to enhanced MHC II levels and aberrant T-cell responses, as seen in mouse models.

Functions in Plants

Hormone Response Pathways

The SCF complex plays a central role in plant hormone signaling by facilitating the ubiquitin-mediated degradation of transcriptional repressors, thereby activating downstream responses. In auxin signaling, the SCF^TIR1/AFB complex functions as the primary receptor. Upon auxin binding, TIR1 or its paralogs (AFB1–AFB5) interact directly with Aux/IAA repressor proteins, promoting their polyubiquitination and subsequent degradation by the 26S proteasome. This relieves repression of auxin response factors (ARFs), enabling the transcription of auxin-responsive genes that regulate processes such as cell elongation, root development, and apical dominance.^[47]^[48] In the jasmonate (JA) pathway, the SCF^COI1 complex similarly acts as a receptor for the bioactive JA species, JA-isoleucine (JA-Ile). JA-Ile binding to COI1 enhances its affinity for JAZ repressor proteins, leading to their ubiquitination and proteasomal degradation. This derepresses the transcription factor MYC2, which activates JA-responsive genes involved in defense, wounding, and male fertility. The mechanism parallels auxin signaling, highlighting the conserved use of SCF complexes in hormone perception.^[49]^[50] TIR1 and COI1 exemplify the structural conservation of F-box proteins in SCF complexes, both featuring leucine-rich repeat (LRR) domains that mediate hormone-induced substrate binding. TIR1's LRR domain directly coordinates auxin, while COI1's LRR similarly recognizes JA-Ile, underscoring the evolutionary adaptation of SCF ligases for small-molecule perception in plants. Genetic studies in Arabidopsis thaliana provide strong evidence for these roles; tir1 mutants exhibit auxin insensitivity, failing to degrade Aux/IAA proteins and showing defects in root gravitropism and lateral root formation. Likewise, coi1 mutants display JA insensitivity, with impaired root growth inhibition and reduced defense gene expression upon wounding.^[47]^[49]^[51]^[50] SCF complexes also integrate with other hormone pathways, such as gibberellin (GA) signaling, where the SCF^GID2 complex in rice targets the DELLA repressor SLR1 for degradation upon GA perception by GID1, promoting stem elongation and seed germination. This cross-talk allows coordinated regulation of growth and stress responses across hormone networks.^[52]

Defense Against Pathogens

The SCF ubiquitin ligase complex plays a crucial role in plant immune responses by targeting specific substrates for degradation, thereby modulating defense mechanisms against pathogens. A 2024 study identified an SCF complex in apple (Malus domestica) that enhances resistance to Valsa mali, the causal agent of Valsa canker, a devastating fungal disease. This complex, involving the F-box protein MdSKIP14, fine-tunes immune responses; knockdown of MdSKIP14 led to increased susceptibility, while overexpression improved resistance.^[53] In pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), SCF complexes contribute to the hypersensitive response (HR), a localized programmed cell death that restricts pathogen spread. For instance, the SCF^{SNIPER7} complex in tomato (Solanum lycopersicum) regulates the turnover of the unfoldase CDC48A, which is essential for HR execution; disruption of this SCF-mediated degradation attenuates HR and compromises resistance to bacterial pathogens, demonstrating how SCF ensures timely immune component disposal during ETI. Similarly, SCF ligases interact with components like SGT1 to initiate HR signaling, integrating ubiquitination into the rapid defense cascade triggered by pathogen recognition.^[54]^[55] Specific F-box proteins within SCF complexes target pattern recognition receptors (PRRs) for ubiquitination, attenuating PTI to prevent excessive signaling. Although PUB13 is a U-box E3 ligase, it exemplifies this mechanism by directly ubiquitinating the PRR FLS2 upon flagellin perception in Arabidopsis thaliana, leading to receptor endocytosis and degradation; this negative feedback limits reactive oxygen species burst and defense gene expression, maintaining immune homeostasis. Analogous F-box proteins, such as CPR1/CPR30, regulate PRR-related signaling by targeting immune regulators, underscoring the broader role of SCF-associated F-boxes in PRR turnover.^[56] The SCF^{COI1} complex intersects with jasmonate (JA) signaling to bolster fungal defense, as COI1 acts as the F-box receptor for JA-isoleucine, promoting degradation of JAZ repressors and activating downstream antifungal responses. In Arabidopsis, SCF^{COI1} mutants exhibit heightened susceptibility to necrotrophic fungi like Botrytis cinerea and Alternaria brassicicola, as JA-mediated defenses, including antimicrobial compound production, are impaired; this overlap enables coordinated signaling against fungal invaders. Hormone pathways, such as those priming JA responses, further amplify SCF-driven defenses.^[57]^[58] Evolutionary adaptations of SCF components in crop plants have enhanced pathogen resistance through diversification of F-box proteins. In crops like apple and rice, expanded F-box gene families, such as those encoding MdSKIP14 or OsFBX156, have evolved under selective pressure from pathogens, enabling substrate-specific ubiquitination that strengthens immunity; phylogenetic analyses reveal duplications and variations in these genes correlating with resistance traits in domesticated lines, facilitating breeding for durable defense.^[59]^[60]

References

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The SCF E3 ubiquitin ligases select specific proteins for ubiquitination (and typically destruction) by coupling variable adaptor (F box) proteins.
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Aug 9, 2021 · The SKP1, CUL1, F-box protein (SCF) complex is an E3 ubiquitin ligase that covalently attaches mono- or poly-ubiquitin chains onto protein ...
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Structure of the Cul1–Rbx1–Skp1–F boxSkp2 SCF ubiquitin ligase ...
Apr 18, 2002 · SCF complexes are the largest family of E3 ubiquitin–protein ligases and mediate the ubiquitination of diverse regulatory and signalling ...Structure Of Cul1 · Cullin Repeats Of The... · Cul1--Skp1--F Box Ternary...
[4]
Identification of an SCF ubiquitin–ligase complex required for auxin ...
We report that in Arabidopsis, auxin response is dependent on a ubiquitin-ligase (E3) complex called SCFTIR1.
[5]
SCF ubiquitin ligase-targeted therapies - PubMed - NIH
This Review explores and discusses potential strategies to target SCF-mediated biological processes to treat human diseases.
[6]
Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ... - PubMed
SCF complexes are the largest family of E3 ubiquitin-protein ligases and mediate the ubiquitination of diverse regulatory and signalling proteins.
[7]
The SCF Complex Is Essential to Maintain Genome and ... - MDPI
Aug 9, 2021 · The SCF complex is composed of three invariable core components, namely RING-box 1 (RBX1), a RING-finger protein that recruits the E2 ubiquitin- ...
[8]
Nedd8 Modification of Cul-1 Activates SCFβTrCP-Dependent ... - NIH
Here we show that Nedd8 modification of the Cul-1 component of SCFβTrCP is important for function of SCFβTrCP in ubiquitination of IκBα. In cells, Nedd8- ...
[9]
Protein neddylation and its role in health and diseases - Nature
Apr 5, 2024 · Cullin neddylation is a complex process requiring the coordinated action of multiple components, including NEDD8, E1, E2, a multifunctional RING ...<|control11|><|separator|>
[10]
Multimodal activation of the ubiquitin ligase SCF by Nedd8 ... - NIH
Conjugation of ubiquitin-like protein Nedd8 to cullin (i.e. neddylation) is essential for the function of cullin-RING ubiquitin ligases (CRLs).
[11]
The F-box protein family | Genome Biology | Full Text - BioMed Central
Nov 10, 2000 · F-box proteins were first characterized as components of SCF ubiquitin-ligase complexes (named after their main components, Skp I, Cullin, and ...Gene Organization And... · Localization And Function · Regulation
[12]
F-Box Proteins and Cancer - MDPI
F-box proteins are responsible for substrate recognition by each SCF complex ... In addition to loss-of-function mutations in the substrate binding domain ...
[13]
Cryo-EM structure of SKP1-SKP2-CKS1 in complex with CDK2 ...
Jul 3, 2023 · Here we describe the experimentally determined structure of the isolated CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex at 3.4 Å global resolution using cryogenic ...
[14]
E3 ubiquitin ligases: styles, structures and functions - PMC
Jul 30, 2021 · Ubiquitination is defined as a series of enzymatic cascades consisting of three crucial enzymes, including E1s, E2s, and E3 ubiquitin ligases.
[15]
Composition and Regulation of the Cellular Repertoire of SCF ...
Nov 30, 2017 · SCF (Skp1-Cullin-F-box) ubiquitin ligases comprise several dozen modular enzymes that have diverse roles in biological regulation.
[16]
Article Mechanism of Lysine 48-Linked Ubiquitin-Chain Synthesis by ...
Dec 16, 2005 · We propose that the acidic loop favorably positions K48 of a substrate-linked ubiquitin to attack SCF bound Cdc34∼ubiquitin thioester and ...
[17]
Structural Insights into NEDD8 Activation of Cullin-RING Ligases
Three independent experiments indicate NEDD8 modification induces related conformational changes for Cul1-Rbx1. First, we performed Small Angle X-ray Scattering ...
[18]
Cand1 Promotes Assembly of New SCF Complexes Through ... - NIH
Cand1 is a protein exchange factor that accelerates the rate at which Cul1–Rbx1 equilibrates with multiple F-box Protein–Skp1 modules.
[19]
Regulation of neddylation and deneddylation of cullin1 in SCF Skp2 ...
Aug 1, 2006 · The extent of the neddylation of cullins is also affected by the COP9/signalosome (CSN) complex, a large multiprotein complex that has a ...
[20]
Molecular mechanisms of CAND2 in regulating SCF ubiquitin ligases
Feb 26, 2025 · We demonstrate that CAND2 promotes SCF-mediated protein degradation as an F-box protein exchange factor.
[21]
Regulation of cell cycle drivers by Cullin-RING ubiquitin ligases
Oct 2, 2020 · In this review, we summarize the structure of CRLs and their functions in driving the cell cycle. We focus on how CRLs target key proteins for degradation.
[22]
SIC1 is ubiquitinated in vitro by a pathway that requires CDC4 ...
Oct 13, 2017 · Traversal from G1 to S-phase in cycling cells of budding yeast is dependent on the destruction of the S-phase cyclin/CDK inhibitor SIC1.
[23]
p27(Kip1) ubiquitination and degradation is regulated by the SCF ...
Phosphorylation of p27 at Thr187 was essential for its degradation. Degradation was also dependent on SCF(Skp2), a protein complex implicated in targeting ...Missing: p21Cip1 | Show results with:p21Cip1
[24]
Role of the SCFSkp2 ubiquitin ligase in the degradation of p21Cip1 ...
Jul 11, 2003 · The cyclin-dependent kinase inhibitor p21Cip1 has important roles in the control of cell proliferation, differentiation, senescence, ...
[25]
Phosphorylation-dependent Ubiquitination of Cyclin E by ... - PubMed
Depletion of Fbw7 leads to accumulation and stabilization of cyclin E in vivo in human and Drosophila melanogaster cells. Multiple F-box proteins contribute to ...
[26]
Prophase Destruction of Emi1 by the SCFβTrCP/Slimb Ubiquitin ...
Here we show that Emi1 destruction and APC activation in early mitosis require the activity of an SCF E3 ubiquitin ligase containing the substrate adaptor ...
[27]
F-Box Protein FBXO31 Mediates Cyclin D1 Degradation to Induce ...
It has been previously shown that G1 arrest following DNA damage occurs in a two-phase response, referred to as initiation and maintenance. The maintenance ...
[28]
The SCFβ-TRCP–ubiquitin ligase complex associates specifically ...
This SCF complex also recognizes a conserved destruction motif in β-catenin, a protein with levels also regulated by phosphorylation-dependent ubiquitination.Missing: seminal | Show results with:seminal
[29]
Signal-induced ubiquitination of IκBα by the F-box protein Slimb/β ...
Upon phosphorylation of IκB by an IκB kinase complex, βTrCP recruits IκBα to the SCF complex, allowing the associated E2, such as Ubch5, to ubiquitinate IκBα.
[30]
A ubiquitin ligase complex essential for the NF-κB, Wnt/Wingless ...
The exciting new finding is that one SCF ligase complex (SCFβTrCP) may ubiquitinate the protein targets in all three signaling pathways (IκBα, β-cat/Arm, and Ci) ...
[31]
Skp2 is oncogenic and overexpressed in human cancers - PubMed
Skp2 protein overexpression may lead to accelerated p27 proteolysis and contribute to malignant progression from dysplasia to oral epithelial carcinoma.
[32]
Clinical significance of FBXW7 loss of function in human cancers
Mar 26, 2022 · Recent evidence shows that genetic mutation of FBXW7 differentially affects the degradation of specific cellular targets resulting in a distinct ...Missing: paper | Show results with:paper
[33]
Beta-Transducin Repeats-Containing Proteins as an Anticancer Target
The increased expression of β-TrCP1 has been reported to confer the constitutive activation of NF-κB in chemoresistant pancreatic cancer cells [98]. The ...Missing: source | Show results with:source
[34]
A patent review of SCF E3 ligases inhibitors for cancer
Nov 15, 2024 · However，SCF E3 ubiquitin ligase is primarily responsible for regulating protein degradation and plays a key role in regulating cell cycle, ...
[35]
PROTACs: Current and Future Potential as a Precision Medicine ...
Importantly, PROTACs have the capacity to target virtually any intracellular and transmembrane protein for degradation, including oncoproteins previously ...
[36]
The F-box protein TIR1 is an auxin receptor - Nature
May 26, 2005 · These results indicate that TIR1 is an auxin receptor that mediates Aux/IAA degradation and auxin-regulated transcription.The Auxin Receptor... · Auxin Binds Directly To Scf · Tir1 Is An Auxin Receptor
[37]
Plant development is regulated by a family of auxin receptor F box ...
Our results indicate that TIR1 and the AFB proteins collectively mediate auxin responses throughout plant development.
[38]
JAZ repressor proteins are targets of the SCF COI1 complex ... - Nature
Jul 18, 2007 · Our results suggest a model in which jasmonate ligands promote the binding of the SCF COI1 ubiquitin ligase to and subsequent degradation of the JAZ1 repressor ...
[39]
COI1 links jasmonate signalling and fertility to the SCF ubiquitin ...
Nov 19, 2002 · COI1 is therefore expected to form a functional E3-type ubiquitin ligase in plants and to regulate expression of jasmonate responsive genes.
[40]
The F-box protein TIR1 is an auxin receptor - PubMed
Recent studies indicate that auxin acts by promoting the degradation of the Aux/IAA transcriptional repressors through the action of the ubiquitin protein ...
[41]
GID2, an F‐box subunit of the SCF E3 complex, specifically interacts ...
Jan 26, 2004 · Summary. The phytohormone gibberellin (GA) controls growth and development in plants. Previously, we identified a rice F-box protein, ...
[42]
Identification of an SCF Ubiquitin Ligase Complex that Contributes ...
Jun 17, 2024 · In this study, we identified an SCF ubiquitin ligase complex that can enhance resistance to Valsa canker in apple. Disease evaluation ...
[43]
SCF SNIPER7 controls protein turnover of unfoldase CDC48A to ...
Nov 6, 2020 · Taken together, this study reveals a new mechanism where a SCFSNIPER7 complex regulates CDC48 unfoldase levels and modulates immune output.Plasmid Construction And... · Results · Scf Boosts Immunity By...
[44]
Role of SCF Ubiquitin-Ligase and the COP9 Signalosome in ... - NIH
This recognition event initiates signaling pathways that lead to hypersensitive response ... Thus, SCF seems to play an important role in plant defense, in ...
[45]
Regulation of plant immune receptors by ubiquitination - Frontiers
The ligase generally acts as a scaffold bringing the E2 and the target into close proximity to mediate the linkage of ubiquitin via its C-terminal glycine to an ...
[46]
The SCFCOI1 Ubiquitin-Ligase Complexes Are Required for ... - NIH
The Arabidopsis COI1 gene that is required for response to jasmonates (JAs), which regulate root growth, pollen fertility, wound healing, and defense against ...Missing: paper | Show results with:paper
[47]
Nuclear jasmonate and salicylate signaling and crosstalk in defense ...
Arabidopsis plants lacking the COI1 gene are more susceptible to necrotrophic pathogens such as Alternaria brassicicola and Botrytis cinerea (Thomma et al., ...
[48]
(PDF) Diverse and dynamic roles of F-box proteins in plant biology
Aug 9, 2025 · The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein ...
[49]
The F‐box protein OsFBX156 positively regulates rice defence ...
May 29, 2024 · ETI often leads to more prolonged and robust resistance to pathogens and a rapid hypersensitive ... 1 negatively regulates the rice PTI response ...