5VZT | pdb_00005vzt

Crystal structure of the Skp1-FBXO31 complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d5vztc2	All alpha proteins	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5vztc1	Alpha and beta proteins (a+b)	POZ domain	POZ domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5vzta2	All alpha proteins	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5vzta1	Alpha and beta proteins (a+b)	POZ domain	POZ domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Skp1 dimerisation domain-like	8038683	3000564	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	POZ domain	8035033	3000894	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)
D		e5vztD1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: Cadherin	F:	ECOD (20:10:01)
B		e5vztB1	A: Lipocalins/Streptavidin	X: Lipocalins	H: Lipocalins	T:	F:	ECOD (20:10:01)
B		e5vztB3	A: Lipocalins/Streptavidin	X: Lipocalins	H: Lipocalins	T: Cyclin_D1_bind	F:	ECOD (20:10:01)
C		e5vztC1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: ATP-synt_VA_C	F:	ECOD (20:10:01)
A		e5vztA1	A: Cryptochrome/photolyase FAD-binding domain-related	X: Cryptochrome/photolyase FAD-binding domain-related	H: PriX	T: Peptidase_M1	F:	ECOD (20:10:01)

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
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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
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 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 ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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
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

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.