4F52 | pdb_00004f52

Structure of a Glomulin-RBX1-CUL1 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)
D	d4f52d_	Small proteins	RING/U-box	RING/U-box	RING finger domain, C3HC4	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4f52b_	Small proteins	RING/U-box	RING/U-box	RING finger domain, C3HC4	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex	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)
D	SCOP2B Superfamily	RING/U-box like	8040866	3000160	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RING/U-box like	8040866	3000160	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8003455	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8003455	3000034	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)
F	Abhydrolase_3	e4f52F1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Abhydrolase_3	ECOD (v294.1)
E	HHH_6	e4f52E1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: HHH_6	ECOD (v294.1)
D	V-set	e4f52D2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: V-set	ECOD (v294.1)
B	Avidin	e4f52B1	A: a/b three-layered sandwiches	X: Globin-like	H: Nucleoside diphosphate kinases	T: Nucleoside diphosphate kinases	F: Avidin	ECOD (v294.1)
C	DIL	e4f52C6	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: DIL	ECOD (v294.1)
A	Avidin	e4f52A2	A: a/b three-layered sandwiches	X: Globin-like	H: Nucleoside diphosphate kinases	T: Nucleoside diphosphate kinases	F: Avidin	ECOD (v294.1)
A	HMGL-like	e4f52A1	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: HMGL-like	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C	1.20.1310.10	Mainly Alpha	Up-down Bundle	5 helical Cullin repeat like	Cullin Repeats	CATH (4.3.0)
C	3.30.230.130	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
A	1.20.1310.10	Mainly Alpha	Up-down Bundle	5 helical Cullin repeat like	Cullin Repeats	CATH (4.3.0)
A	3.30.230.130	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F	PF08568	Uncharacterised protein family, YAP/Alf4/glomulin (Kinetochor_Ybp2)	Uncharacterised protein family, YAP/Alf4/glomulin	-	Repeat
B, D	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
A, C	PF26557	Cullin alpha+beta domain (Cullin_AB)	Cullin alpha+beta domain	This entry represents the alpha+beta domain found just before the C-terminal domain of Cullin proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	Glomulin	enzyme regulator activity molecular function inhibitor activity ubiquitin-protein transferase regulator activity ubiquitin-protein transferase inhibitor activity molecular function regulator activity enzyme inhibitor activity protein binding binding signaling receptor binding growth factor receptor binding hepatocyte growth factor receptor binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication cellular developmental process blood vessel morphogenesis vasculogenesis vasculature development circulatory system development cell differentiation blood vessel development negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of interleukin-2 production interleukin-2 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of interleukin-2 production regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process modification-dependent macromolecule catabolic process protein metabolic process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process muscle structure development muscle cell differentiation epigenetic regulation of gene expression cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis positive regulation of phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of phosphate metabolic process phosphate-containing compound metabolic process regulation of phosphorus metabolic process regulation of phosphorylation phosphorus metabolic process negative regulation of lymphocyte proliferation regulation of leukocyte activation regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of immune system process regulation of leukocyte proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation regulation of cell adhesion cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of immune system process immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation	cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex Cul3-RING ubiquitin ligase complex Cul4-RING E3 ubiquitin ligase complex Cul4A-RING E3 ubiquitin ligase complex cellular anatomical structure intracellular anatomical structure cytoplasm Cul2-RING ubiquitin ligase complex
B, D	E3 ubiquitin-protein ligase RBX1	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein-containing complex binding binding molecular adaptor activity ubiquitin protein ligase binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein-containing complex binding binding molecular adaptor activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cullin family protein binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NEDD8 transferase activity NEDD8 ligase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion biological regulation regulation of mitophagy regulation of catabolic process negative regulation of mitophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy metabolic process regulation of metabolic process autophagy of mitochondrion multicellular organismal process negative regulation of type I interferon production cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process type I interferon production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of type I interferon production developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation protein polyubiquitination primary metabolic process protein K27-linked ubiquitination protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process transcription-coupled nucleotide-excision repair DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleotide-excision repair DNA repair response to oxidative stress regulation of response to stress regulation of response to oxidative stress negative regulation of response to oxidative stress cellular response to chemical stimulus response to chemical cellular response to oxidative stress cellular response to chemical stress intracellular signal transduction intracellular signaling cassette MAPK cascade cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway regulation of cellular response to insulin stimulus cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus response to endogenous stimulus regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound negative regulation of cellular response to insulin stimulus negative regulation of insulin receptor signaling pathway response to insulin cellular response to insulin stimulus ubiquitin-dependent protein catabolic process via the C-end degron rule pathway cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid protein K48-linked ubiquitination protein monoubiquitination positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction positive regulation of signaling RNA metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II RNA surveillance RNA catabolic process transcription initiation at RNA polymerase II promoter RNA polymerase II transcription initiation surveillance nuclear RNA surveillance nucleobase-containing compound biosynthetic process DNA-templated transcription initiation nucleobase-containing compound catabolic process nucleic acid catabolic process signal transduction in response to DNA damage negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction protein neddylation SCF-dependent proteasomal ubiquitin-dependent protein catabolic process regulation of protein modification process regulation of protein autoubiquitination regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of protein modification process 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 post-translational protein modification protein autoubiquitination positive regulation of protein autoubiquitination positive regulation of TORC1 signaling positive regulation of TOR signaling regulation of TORC1 signaling TOR signaling regulation of TOR signaling TORC1 signaling T cell activation immune system process cell activation lymphocyte activation leukocyte activation response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV fat cell differentiation regulation of developmental process cellular developmental process negative regulation of developmental process regulation of cell differentiation negative regulation of fat cell differentiation negative regulation of beige fat cell differentiation cell differentiation beige fat cell differentiation negative regulation of cell differentiation regulation of fat cell differentiation	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 intracellular organelle centrosome microtubule organizing center cytoskeleton 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 intracellular organelle centrosome microtubule organizing center cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasmic ubiquitin ligase complex VCB complex Cul5-RING ubiquitin ligase complex Cul4-RING E3 ubiquitin ligase complex Cul4A-RING E3 ubiquitin ligase complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen SCF ubiquitin ligase complex Cul7-RING ubiquitin ligase complex Cul3-RING ubiquitin ligase complex Cul4B-RING E3 ubiquitin ligase complex site of DNA damage chromosome Cul2-RING ubiquitin ligase complex
A, C	Cullin-1	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling developmental process anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis cell death apoptotic signaling pathway apoptotic process intrinsic apoptotic signaling pathway programmed cell death cell population proliferation 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 response to oxidative stress cellular response to chemical stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress protein polyubiquitination protein K48-linked ubiquitination 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 protein monoubiquitination	cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane Parkin-FBXW7-Cul1 ubiquitin ligase complex cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane Parkin-FBXW7-Cul1 ubiquitin ligase complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen SCF ubiquitin ligase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR013877	YAP-binding/ALF4/Glomulin	Family
E, F	IPR019516	Glomulin/ALF4	Family
B, D	IPR051031	RING-box E3 Ubiquitin Ligase	Family
B, D	IPR024766	Zinc finger, RING-H2-type	Domain
B, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B, D	IPR001841	Zinc finger, RING-type	Domain
A, C	IPR045093	Cullin	Family
A, C	IPR016158	Cullin homology domain	Domain
A, C	IPR016157	Cullin, conserved site	Conserved Site
A, C	IPR059120	Cullin-like, alpha+beta domain	Domain
A, C	IPR001373	Cullin, N-terminal	Domain
A, C	IPR019559	Cullin, neddylation domain	Domain
A, C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, C	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, C	IPR036317	Cullin homology domain superfamily	Homologous Superfamily
A, C	IPR016159	Cullin repeat-like-containing domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F	Pharos: Q92990	glomuvenous malformation astrocytic tumor glomangioma lung cancer cerebrovascular disorder oligodendroglioma glioblastoma intellectual disability
B, D	Pharos: P62877	Stevens-Johnson syndrome acute myeloid leukemia Drug-Induced Stevens Johnson Syndrome ovarian cancer toxic epidermal necrolysis astrocytic tumor endogenous depression Crohn disease
A, C	Pharos: Q13616	Stevens-Johnson syndrome Drug-Induced Stevens Johnson Syndrome ovarian cancer toxic epidermal necrolysis inflammatory bowel disease

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.