5VZU | pdb_00005vzu

Crystal structure of the Skp1-FBXO31-cyclin D1 complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	POZ domain	8035033	3000894	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Skp1 dimerisation domain-like	8038683	3000564	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Skp1 dimerisation domain-like	8038683	3000564	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	POZ domain	8035033	3000894	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	SBP_bac_1	e5vzuC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SBP_bac_1	ECOD (v294.1)
A	SBP_bac_1	e5vzuA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SBP_bac_1	ECOD (v294.1)
D		e5vzuD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Parafibromin N-terminal domain	T: Parafibromin N-terminal domain	F:	ECOD (v294.1)
B		e5vzuB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Parafibromin N-terminal domain	T: Parafibromin N-terminal domain	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)
A	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation domain		Domain
A, C	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain		Domain
B, D	PF12014	Cyclin D1 binding domain (Cyclin_D1_bind)	Cyclin D1 binding domain	Ubiquitin-dependent proteolysis of cyclin D1 is associated with normal and tumour cell proliferation and survival. The best characterised member of this family is the SCF FBXO31 (Skp1-Cul1-Rbx1-FBXO31) ubiquitin ligase complex mediates genotoxic stre ...	Ubiquitin-dependent proteolysis of cyclin D1 is associated with normal and tumour cell proliferation and survival. The best characterised member of this family is the SCF FBXO31 (Skp1-Cul1-Rbx1-FBXO31) ubiquitin ligase complex mediates genotoxic stress-induced cyclin D1 degradation [1]. FBXO31 possesses a unique substrate-binding beta barrel domain, whereas cyclin D1 binds to FBXO31 by tucking its free C-terminal carboxylate tail into an open cavity of the C-terminal FBXO31 beta-barrel. Biophysical and functional studies demonstrated that SCFFBXO31 is capable of recruiting and ubiquitinating cyclin D1 in a phosphorylation-independent manner.	Domain
B, D	PF12937	F-box-like (F-box-like)	F-box-like	This is an F-box-like family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	S-phase kinase-associated protein 1	protein complex scaffold activity ubiquitin ligase complex scaffold activity structural molecule activity protein binding binding protein domain specific binding enzyme regulator activity ubiquitin ligase activator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity cullin family protein binding protein complex scaffold activity ubiquitin ligase complex scaffold activity structural molecule activity protein binding binding protein domain specific binding enzyme regulator activity ubiquitin ligase activator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity cullin family protein binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity beta-catenin binding F-box domain binding	maintenance of protein location cellular localization maintenance of protein location in nucleus protein localization to nucleus maintenance of location maintenance of location in cell localization maintenance of protein location in cell macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle intracellular protein localization primary metabolic process maintenance of protein location cellular localization maintenance of protein location in nucleus protein localization to nucleus maintenance of location maintenance of location in cell localization maintenance of protein location in cell macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle intracellular protein localization primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process protein polyubiquitination protein K48-linked ubiquitination protein monoubiquitination cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex centrosome microtubule organizing center cytoskeleton membraneless organelle membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cullin-RING ubiquitin ligase complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul7-RING ubiquitin ligase complex
B, D	F-box only protein 31	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding cyclin binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication signal transduction in response to DNA damage signal transduction cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication signal transduction in response to DNA damage signal transduction catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process anaphase-promoting complex-dependent catabolic process ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal SCF-dependent proteasomal ubiquitin-dependent protein catabolic process regulation of cell cycle phase transition DNA damage checkpoint signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic G1 DNA damage checkpoint signaling mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle mitotic cell cycle phase transition response to oxidative stress cellular response to chemical stimulus response to chemical cellular response to oxidative stress cellular response to chemical stress	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol somatodendritic compartment cell body intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol somatodendritic compartment cell body neuronal cell body cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex
E, F	Cyclin D1	histone deacetylase binding protein binding binding enzyme binding proline-rich region binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein-containing complex binding enzyme regulator activity histone deacetylase binding protein binding binding enzyme binding proline-rich region binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein-containing complex binding enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity cyclin-dependent protein serine/threonine kinase activator activity cyclin-dependent protein kinase regulator activity cyclin-dependent protein serine/threonine kinase regulator activity transcription corepressor activity transcription regulator activity transcription coregulator activity kinase binding protein kinase binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to chemical response to xenobiotic stimulus response to metal ion response to calcium ion cell division response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to chemical response to xenobiotic stimulus response to metal ion response to calcium ion cell division response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus response to hypoxia response to oxygen levels response to abiotic stimulus response to X-ray response to ionizing radiation response to radiation regulation of cellular process regulation of cell cycle phase transition DNA damage checkpoint signaling signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling regulation of biological process negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition biological regulation DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic G1 DNA damage checkpoint signaling mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle signal transduction in response to DNA damage G1/S transition of mitotic cell cycle mitotic cell cycle phase transition response to iron ion positive regulation of biological process positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle positive regulation of cellular process positive regulation of G1/S transition of mitotic cell cycle positive regulation of cell cycle positive regulation of cell cycle G1/S phase transition positive regulation of cell cycle phase transition response to ketone response to lipid response to endogenous stimulus response to alcohol response to glucocorticoid response to oxygen-containing compound response to corticosterone response to mineralocorticoid response to corticosteroid response to hormone response to steroid hormone response to light stimulus response to UV response to UV-A multicellular organismal process regulation of developmental process positive regulation of cell population proliferation mammary gland development gland development positive regulation of mammary gland epithelial cell proliferation positive regulation of developmental process anatomical structure development regulation of multicellular organismal process epithelial cell proliferation developmental process epithelium development cell population proliferation positive regulation of epithelial cell proliferation animal organ development tissue development regulation of mammary gland epithelial cell proliferation mammary gland epithelium development regulation of cell population proliferation positive regulation of multicellular organismal process regulation of epithelial cell proliferation mammary gland epithelial cell proliferation fat cell differentiation cellular developmental process cell differentiation regulation of body fluid levels secretion transport establishment of localization body fluid secretion localization lactation regulation of biological quality re-entry into mitotic cell cycle response to nutrient levels response to nutrient response to vitamin E response to vitamin RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to leptin cellular response to topologically incorrect protein endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein response to topologically incorrect protein response to endoplasmic reticulum stress gonad development reproductive system development reproductive process sex differentiation developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics reproductive structure development Leydig cell differentiation system development response to estrogen regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation negative regulation of cell differentiation regulation of multicellular organismal development negative regulation of epithelial cell differentiation negative regulation of developmental process animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration nervous system development generation of neurons neurogenesis neuron differentiation neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of neuron apoptotic process response to ethanol cell surface receptor signaling pathway Wnt signaling pathway G2/M transition of mitotic cell cycle cell cycle G2/M phase transition positive regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition mammary gland lobule development mammary gland alveolus development response to estradiol response to magnesium ion	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm cytosol cyclin D1-CDK4 complex cyclin D1-CDK6 complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton transcription regulator complex transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR016073	SKP1 component, POZ domain	Domain
A, C	IPR001232	S-phase kinase-associated protein 1-like	Family
A, C	IPR036296	SKP1-like, dimerisation domain superfamily	Homologous Superfamily
A, C	IPR016072	SKP1 component, dimerisation	Domain
A, C	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
A, C	IPR016897	S-phase kinase-associated protein 1	Family
B, D	IPR036047	F-box-like domain superfamily	Homologous Superfamily
B, D	IPR045048	F-box only protein 31/39	Family
B, D	IPR001810	F-box domain	Domain
E, F	IPR048258	Cyclins, cyclin-box	Conserved Site
E, F	IPR004367	Cyclin, C-terminal domain	Domain
E, F	IPR006671	Cyclin, N-terminal	Domain
E, F	IPR036915	Cyclin-like superfamily	Homologous Superfamily
E, F	IPR039361	Cyclin	Family
E, F	IPR013763	Cyclin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P63208	allergic rhinitis esophageal adenocarcinoma hypothyroidism medulloblastoma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma ovarian cancer plasma cell myeloma systemic lupus erythematosus breast cancer Hashimoto thyroiditis malignant glioma allergic rhinitis esophageal adenocarcinoma hypothyroidism medulloblastoma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma ovarian cancer plasma cell myeloma systemic lupus erythematosus breast cancer Hashimoto thyroiditis malignant glioma pancreatic ductal adenocarcinoma rheumatoid arthritis
B, D	Pharos: Q5XUX0	intellectual disability, autosomal recessive 45 atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma ovarian cancer breast cancer intellectual disability malignant ependymoma pituitary cancer gastric carcinoma malignant glioma subependymal giant cell astrocytoma
E, F	Pharos: P24385	plasma cell myeloma von Hippel-Lindau disease angiosarcoma transitional cell carcinoma breast cancer cancer leukemia breast carcinoma hyperparathyroidism squamous cell carcinoma nasopharyngeal carcinoma esophageal squamous cell carcinoma B-cell chronic lymphocytic leukemia mantle cell lymphoma malignant colon neoplasm plasma cell myeloma von Hippel-Lindau disease angiosarcoma transitional cell carcinoma breast cancer cancer leukemia breast carcinoma hyperparathyroidism squamous cell carcinoma nasopharyngeal carcinoma esophageal squamous cell carcinoma B-cell chronic lymphocytic leukemia mantle cell lymphoma malignant colon neoplasm hepatocellular carcinoma prostate cancer Mammary Neoplasms, Experimental salivary gland cancer kidney cancer adenocarcinoma adenoid cystic carcinoma squamous papilloma esophageal cancer thyroid adenoma granular cell carcinoma cecal neoplasm cervical cancer melanoma liver cancer brain cancer papilloma carcinoma cecum cancer hyperplasia salivary gland adenoid cystic carcinoma sarcomatoid carcinoma cutaneous melanoma thyroid gland carcinoma gastric cancer tubular adenocarcinoma hereditary diffuse gastric adenocarcinoma hydrolethalus syndrome psoriasis intestinal disease colorectal cancer medulloblastoma cribriform carcinoma schizophrenia myocardial ischemia cystic fibrosis liver disease lung benign neoplasm atypical teratoid rhabdoid tumor oligodendroglioma eye disease benign colon neoplasm bone disease ovarian disease gastric neoplasm undifferentiated carcinoma major depressive disorder pilocytic astrocytoma malignant ependymoma plasma cell neoplasm prostate disease intestinal polyp kidney neoplasm cribriform carcinoma of breast adenoma endometrial cancer stomach disease liver neoplasm thyroid cancer lung cancer osteosarcoma lymphatic system disease male breast carcinoma pituitary cancer hematologic disease uterine disease malignant glioma breast disease precancerous condition malignant mesothelioma primitive neuroectodermal tumor mammary neoplasms, animal colonic neoplasm coronary artery disease large cell medulloblastoma myeloid neoplasm neoplasm of esophagus endometrial carcinoma subependymal giant cell astrocytoma astrocytic tumor lung disease ovarian cancer benign urinary system neoplasm brain disease papillomatosis glioblastoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.