6V9I | pdb_00006v9i

cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2)

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth C]	Cullin_Nedd8	e6v9iC4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Cullin_Nedd8	ECOD (1.6)
A [auth C]	Cullin_4th	e6v9iC3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Cullin_4th	ECOD (1.6)
A [auth C]	Cullin_1st	e6v9iC5	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Cullin_1st	ECOD (1.6)
A [auth C]	Cullin_2nd	e6v9iC2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Cullin_2nd	ECOD (1.6)
A [auth C]	Cullin_3rd	e6v9iC1	A: a+b duplicates or obligate multimers	X: a+b domain in cullin-like proteins (From Topology)	H: a+b domain in cullin-like proteins (From Topology)	T: a+b domain in cullin-like proteins	F: Cullin_3rd	ECOD (1.6)
B [auth R]	zf-rbx1	e6v9iR1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-rbx1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C]	PF00888	Cullin family (Cullin)	Cullin family	-	Repeat
A [auth C]	PF10557	Cullin protein neddylation domain (Cullin_Nedd8)	Cullin protein neddylation domain	This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cu ...	This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue [1].	Domain
B [auth R]	PF12678	RING-H2 zinc finger domain (zf-rbx1)	RING-H2 zinc finger domain	There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell ...	There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	Immunoglobulin G-binding protein G,Cullin-5	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity molecular transducer activity signaling receptor activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity molecular transducer activity signaling receptor activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity calcium channel activity monoatomic cation transmembrane transporter activity monoatomic ion channel activity monoatomic cation channel activity passive transmembrane transporter activity calcium ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity channel activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity protein-containing complex binding immunoglobulin binding IgG binding	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell death intracellular signal transduction cell communication apoptotic signaling pathway cellular process signal transduction apoptotic process intrinsic apoptotic signaling pathway cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell death intracellular signal transduction cell communication apoptotic signaling pathway cellular process signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death 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 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 developmental process multicellular organismal process regulation of cell motility neuron migration cellular developmental process nervous system development regulation of neuron migration generation of neurons neurogenesis multicellular organism development cell differentiation regulation of locomotion anatomical structure development regulation of cell migration cell migration cell motility locomotion system development ERBB2 signaling pathway cell surface receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway ERBB signaling pathway enzyme-linked receptor protein signaling pathway protein K11-linked ubiquitination protein polyubiquitination reelin-mediated signaling pathway mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex Cul5-RING ubiquitin ligase complex SCF ubiquitin ligase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex Cul5-RING ubiquitin ligase complex SCF ubiquitin ligase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome extracellular region
B [auth R]	RING-box protein 2	protein binding binding cullin family protein binding aminoacyltransferase activity ubiquitin-like protein transferase activity NEDD8 transferase activity catalytic activity, acting on a protein acyltransferase activity NEDD8 ligase activity ubiquitin-like protein ligase activity transferase activity catalytic activity cation binding transition metal ion binding protein binding binding cullin family protein binding aminoacyltransferase activity ubiquitin-like protein transferase activity NEDD8 transferase activity catalytic activity, acting on a protein acyltransferase activity NEDD8 ligase activity ubiquitin-like protein ligase activity transferase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding ubiquitin protein ligase activity ubiquitin-protein transferase activity	developmental process multicellular organismal process head development animal organ development brain development nervous system development radial glia guided migration of Purkinje cell multicellular organism development hindbrain radial glia guided cell migration central nervous system development anatomical structure development cell migration cellular process cell motility developmental process multicellular organismal process head development animal organ development brain development nervous system development radial glia guided migration of Purkinje cell multicellular organism development hindbrain radial glia guided cell migration central nervous system development anatomical structure development cell migration cellular process cell motility hindbrain development cell migration in hindbrain system development cellular component organization organelle organization apoptotic mitochondrial changes apoptotic process cellular component organization or biogenesis cell death programmed cell death mitochondrion organization cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication reelin-mediated signaling pathway signal transduction negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process primary metabolic process macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal protein ubiquitination cerebral cortex cell migration forebrain development cerebral cortex radially oriented cell migration pallium development cerebral cortex development telencephalon cell migration forebrain cell migration telencephalon development intrinsic apoptotic signaling pathway in response to oxidative stress intracellular signal transduction apoptotic signaling pathway intrinsic apoptotic signaling pathway regulation of cell motility neuron migration cellular developmental process regulation of neuron migration generation of neurons neurogenesis cell differentiation regulation of locomotion regulation of cell migration locomotion 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 ubiquitin-dependent protein catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex Cul5-RING ubiquitin ligase complex membrane-bounded organelle intracellular organelle organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex Cul5-RING ubiquitin ligase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C]	IPR045093	Cullin	Family
A [auth C]	IPR019559	Cullin protein, neddylation domain	Domain
A [auth C]	IPR016158	Cullin homology domain	Domain
A [auth C]	IPR016157	Cullin, conserved site	Conserved Site
A [auth C]	IPR001373	Cullin, N-terminal	Domain
A [auth C]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A [auth C]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A [auth C]	IPR036317	Cullin homology domain superfamily	Homologous Superfamily
A [auth C]	IPR016159	Cullin repeat-like-containing domain superfamily	Homologous Superfamily
A [auth C]	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
A [auth C]	IPR019950	M protein-type anchor domain	Domain
A [auth C]	IPR005877	YSIRK Gram-positive signal peptide	Domain
A [auth C]	IPR000724	IgG-binding B	Domain
A [auth C]	IPR035152	GA-like domain	Domain
A [auth C]	IPR019931	LPXTG cell wall anchor domain	Domain
B [auth R]	IPR051031	RING-box E3 Ubiquitin Ligase	Family
B [auth R]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B [auth R]	IPR024766	Zinc finger, RING-H2-type	Domain
B [auth R]	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C]	Pharos: Q93034	breast carcinoma breast cancer malignant mesothelioma Mammary Neoplasms, Human plasma cell myeloma osteosarcoma psoriasis lymphoplasmacytic lymphoma ovarian cancer 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.