5VZU

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)
A	SCOP2B Superfamily	Skp1 dimerisation domain-like	8038683	3000564	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	POZ domain	8035033	3000894	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	POZ domain	8035033	3000894	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Skp1 dimerisation domain-like	8038683	3000564	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)
A	PF01466,PF03931	e5vzuA1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: PF01466,PF03931	ECOD (1.6)
C	PF01466,PF03931	e5vzuC1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: PF01466,PF03931	ECOD (1.6)
B	F_UNCLASSIFIED	e5vzuB2	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF12014	e5vzuB1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: PF12014	ECOD (1.6)
B	PF12937	e5vzuB3	A: alpha arrays	X: F-box domain (From Topology)	H: F-box domain (From Topology)	T: F-box domain	F: PF12937	ECOD (1.6)
D	F_UNCLASSIFIED	e5vzuD3	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF12014	e5vzuD2	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: PF12014	ECOD (1.6)
D	PF12937	e5vzuD1	A: alpha arrays	X: F-box domain (From Topology)	H: F-box domain (From Topology)	T: F-box domain	F: PF12937	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)
C	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	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain	-	Domain
A, C	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation 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	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding protein domain specific binding cullin family protein binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity molecular function activator activity molecular function regulator activity beta-catenin binding F-box domain binding	maintenance of protein location protein localization 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 cellular macromolecule localization macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle maintenance of protein location protein localization 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 cellular macromolecule localization macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle organonitrogen compound metabolic process primary metabolic process organic substance 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 organonitrogen compound catabolic process catabolic process proteolysis involved in protein 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 proteolysis SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process regulation of protein modification process regulation of catalytic activity positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination regulation of transferase activity positive regulation of post-translational protein modification regulation of primary metabolic process regulation of ubiquitin protein ligase activity positive regulation of metabolic process positive regulation of molecular function positive regulation of ubiquitin protein ligase activity positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of ubiquitin-protein transferase activity regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process positive regulation of transferase activity regulation of post-translational protein modification regulation of protein metabolic process biological regulation positive regulation of catalytic activity regulation of macromolecule metabolic process positive regulation of ubiquitin-protein transferase activity regulation of molecular function regulation of metabolic process protein polyubiquitination protein K48-linked ubiquitination protein monoubiquitination protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle 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	protein binding binding cyclin binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process organonitrogen compound metabolic process primary metabolic process organic substance metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process organonitrogen compound metabolic process primary metabolic process organic substance 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 organonitrogen compound catabolic process catabolic process proteolysis involved in protein 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 proteolysis anaphase-promoting complex-dependent catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process 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	intracellular anatomical structure cytoplasm cellular anatomical entity 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 cyclin-dependent protein serine/threonine kinase activator activity enzyme regulator activity protein serine/threonine kinase activator activity molecular function activator activity protein kinase regulator activity kinase activator activity enzyme activator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase activator activity histone deacetylase binding protein binding binding enzyme binding cyclin-dependent protein serine/threonine kinase activator activity enzyme regulator activity protein serine/threonine kinase activator activity molecular function activator activity protein kinase regulator activity kinase activator activity enzyme activator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase activator activity kinase regulator activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity proline-rich region binding kinase binding protein kinase 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	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 cell division multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process 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 cell division multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation multicellular organism development cell differentiation anatomical structure development negative regulation of cellular process regulation of multicellular organismal process negative regulation of cell differentiation developmental process epithelium development regulation of biological process regulation of multicellular organismal development negative regulation of epithelial cell differentiation negative regulation of developmental process biological regulation tissue development gland development animal organ development animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration system development nervous system development generation of neurons neurogenesis neuron differentiation positive regulation of phosphorylation regulation of catalytic activity regulation of cyclin-dependent protein kinase activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein serine/threonine kinase activity positive regulation of cyclin-dependent protein serine/threonine kinase activity regulation of phosphate metabolic process regulation of cyclin-dependent protein serine/threonine kinase activity phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process cell cycle phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process positive regulation of cyclin-dependent protein kinase activity positive regulation of cellular metabolic process positive regulation of molecular function positive regulation of protein modification process organic substance metabolic process protein metabolic process positive regulation of protein kinase activity regulation of cell cycle positive regulation of cellular process organonitrogen compound metabolic process positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process positive regulation of cell cycle regulation of phosphorylation cell population proliferation mammary gland development mammary gland epithelium development epithelial cell proliferation mammary gland epithelial cell proliferation regulation of cell cycle phase transition DNA damage checkpoint signaling signaling 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 cell cycle phase transition signal transduction 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 signal transduction in response to DNA damage G1/S transition of mitotic cell cycle mitotic cell cycle phase transition 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 light stimulus response to radiation response to abiotic stimulus response to UV response to UV-A positive regulation of cell population proliferation positive regulation of mammary gland epithelial cell proliferation positive regulation of developmental process positive regulation of epithelial cell proliferation regulation of mammary gland epithelial cell proliferation regulation of cell population proliferation positive regulation of multicellular organismal process regulation of epithelial cell proliferation fat 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 cell surface receptor signaling pathway Wnt signaling pathway negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic 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 negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process response to organic substance response to hormone response to endogenous stimulus response to leptin G2/M transition of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation 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 positive regulation of cell cycle phase transition cellular response to topologically incorrect protein endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein cellular response to chemical stimulus response to topologically incorrect protein cellular response to organic substance response to endoplasmic reticulum stress mammary gland lobule development mammary gland alveolus development	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 cellular anatomical entity intracellular membrane-bounded organelle 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 cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cyclin D1-CDK4 complex cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction 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 salivary gland cancer kidney cancer adenocarcinoma Mammary Neoplasms, Experimental adenoid cystic carcinoma squamous papilloma esophageal cancer thyroid adenoma granular cell carcinoma cecal neoplasm cervical cancer liver cancer melanoma brain cancer papilloma carcinoma hyperplasia cecum cancer 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 schizophrenia medulloblastoma cribriform carcinoma liver disease myocardial ischemia cystic fibrosis lung benign neoplasm atypical teratoid rhabdoid tumor eye disease benign colon neoplasm oligodendroglioma gastric neoplasm undifferentiated carcinoma major depressive disorder bone disease ovarian disease malignant ependymoma pilocytic astrocytoma plasma cell neoplasm prostate disease intestinal polyp kidney neoplasm adenoma cribriform carcinoma of breast endometrial cancer stomach disease liver neoplasm thyroid cancer lung cancer lymphatic system disease osteosarcoma male breast carcinoma pituitary cancer hematologic disease uterine disease malignant glioma precancerous condition malignant mesothelioma breast disease primitive neuroectodermal tumor mammary neoplasms, animal colonic neoplasm large cell medulloblastoma coronary artery disease myeloid neoplasm endometrial carcinoma subependymal giant cell astrocytoma astrocytic tumor neoplasm of esophagus lung disease benign urinary system neoplasm ovarian cancer glioblastoma brain disease papillomatosis

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 National Science Foundation (DBI-1832184), 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 R01GM133198.