3RPG | pdb_00003rpg

Bmi1/Ring1b-UbcH5c complex structure

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)
A	d3rpga1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3rpga2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
B	SCOP2 Family	RING finger domain, C3HC4	8079704	4000374	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RING/U-box like	8079705	3000160	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	UBC-like	8033550	3000570	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		e3rpgC1	A: Cystatin-like	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: zf-C3HC4_2	F:	ECOD (20:10:01)
B		e3rpgB1	A: Cystatin-like	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: zf-C3HC4_2	F:	ECOD (20:10:01)
A		e3rpgA1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: FeoB_Cyto	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	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)
A	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF13923	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_2)	Zinc finger, C3HC4 type (RING finger)		Domain
B	PF13923	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_2)	Zinc finger, C3HC4 type (RING finger)		Domain
A	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	E3 ubiquitin-protein ligase RING2	protein binding binding RING-like zinc finger domain binding protein domain specific binding chromatin binding aminoacyltransferase activity histone H2A ubiquitin ligase activity catalytic activity, acting on a protein acyltransferase activity histone H2AK119 ubiquitin ligase activity transferase activity histone ubiquitin ligase activity ubiquitin-protein transferase activity ubiquitin-like protein transferase activity protein binding binding RING-like zinc finger domain binding protein domain specific binding chromatin binding aminoacyltransferase activity histone H2A ubiquitin ligase activity catalytic activity, acting on a protein acyltransferase activity histone H2AK119 ubiquitin ligase activity transferase activity histone ubiquitin ligase activity ubiquitin-protein transferase activity ubiquitin-like protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity histone modifying activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular process cell cycle mitotic cell cycle developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis gastrulation with mouth forming second embryonic morphogenesis anatomical structure development embryo development gastrulation sexual reproduction cellular developmental process cellular process cell cycle mitotic cell cycle developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis gastrulation with mouth forming second embryonic morphogenesis anatomical structure development embryo development gastrulation sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation cell differentiation germ cell development regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of metabolic process primary metabolic process 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 anterior/posterior axis specification anterior/posterior pattern specification pattern specification process axis specification regionalization negative regulation of biological process 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 cellular process 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	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 sex chromosome intracellular membraneless organelle chromatin chromosome 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 sex chromosome intracellular membraneless organelle chromatin chromosome heterochromatin sex chromatin membraneless organelle PRC1 complex ubiquitin ligase complex catalytic complex transferase complex nuclear ubiquitin ligase complex intracellular protein-containing complex cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen euchromatin nuclear body histone methyltransferase complex MLL1/2 complex MLL1 complex methyltransferase complex
B	Polycomb complex protein BMI-1	enzyme regulator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity protein binding binding RING-like zinc finger domain binding protein domain specific binding chromatin binding promoter-specific chromatin binding cation binding transition metal ion binding enzyme regulator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity protein binding binding RING-like zinc finger domain binding protein domain specific binding chromatin binding promoter-specific chromatin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process multicellular organism development multicellular organismal process segmentation anatomical structure development pattern specification process regionalization segment specification head development central nervous system development animal organ development brain development nervous system development system development developmental process multicellular organism development multicellular organismal process segmentation anatomical structure development pattern specification process regionalization segment specification head development central nervous system development animal organ development brain development nervous system development system development humoral immune response response to stimulus immune response immune system process regulation of cellular 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 positive regulation of molecular function positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of ubiquitin-protein transferase activity protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation positive regulation of catalytic activity primary metabolic process regulation of macromolecule metabolic process positive regulation of ubiquitin-protein transferase activity regulation of molecular function macromolecule modification metabolic process cellular process macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal fibroblast proliferation cell population proliferation positive regulation of cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation regulation of biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process cellular developmental process hemopoiesis cell differentiation cell development embryonic organ morphogenesis chordate embryonic development embryonic morphogenesis embryo development anatomical structure morphogenesis embryo development ending in birth or egg hatching skeletal system development animal organ morphogenesis embryonic skeletal system development skeletal system morphogenesis embryonic organ development embryonic skeletal system morphogenesis cellular response to stimulus response to ketone response to lipid cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to ketone cellular response to steroid hormone stimulus cellular response to hormone stimulus response to endogenous stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to glucocorticoid stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid cellular response to chemical stimulus response to chemical cellular response to lipid response to dexamethasone negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process epigenetic regulation of gene expression negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic in utero embryonic development cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation negative regulation of signaling signaling regulation of signal transduction regulation of programmed cell death negative regulation of cell communication cell communication negative regulation of apoptotic signaling pathway signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway epithelium development neural tube development tube development anterior/posterior pattern specification tissue development rostrocaudal neural tube patterning neural tube patterning positive regulation of B cell proliferation regulation of leukocyte activation regulation of cell activation lymphocyte activation leukocyte proliferation leukocyte activation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of immune system process regulation of multicellular organismal process positive regulation of immune system process regulation of lymphocyte proliferation regulation of leukocyte proliferation B cell activation cell activation positive regulation of lymphocyte proliferation B cell proliferation positive regulation of B cell activation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation positive regulation of multicellular organismal process regulation of lymphocyte activation regulation of developmental process regulation of kidney development renal system development kidney development somatic stem cell division stem cell division cell division RNA 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 regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process regulation of adaxial/abaxial pattern formation adaxial/abaxial pattern specification mononuclear cell differentiation lymphocyte differentiation T cell differentiation in thymus T cell activation regulation of immature T cell proliferation T cell differentiation positive regulation of T cell activation positive regulation of immature T cell proliferation regulation of immature T cell proliferation in thymus positive regulation of T cell proliferation regulation of leukocyte cell-cell adhesion leukocyte differentiation immature T cell proliferation in thymus positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion positive regulation of immature T cell proliferation in thymus T cell proliferation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation immature T cell proliferation regulation of T cell proliferation response to peptide cellular response to interleukin-1 response to cytokine cellular response to cytokine stimulus response to interleukin-1	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 cytoplasm cytosol PRC1 complex ubiquitin ligase complex 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 cytoplasm cytosol PRC1 complex ubiquitin ligase complex catalytic complex transferase complex nuclear ubiquitin ligase complex intracellular protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin nuclear body
A	Ubiquitin-conjugating enzyme E2 D3	ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity binding adenyl ribonucleotide binding nucleotide binding ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process apoptotic process cell death programmed cell death protein autoubiquitination protein ubiquitination post-translational protein modification protein modification by small protein conjugation macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process apoptotic process cell death programmed cell death protein autoubiquitination protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus response to stimulus signaling negative regulation of signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway negative regulation of cell communication cell communication cellular response to endogenous stimulus negative regulation of cellular process signal transduction BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of BMP signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of signal transduction response to BMP regulation of response to stimulus regulation of cell communication transforming growth factor beta receptor superfamily signaling pathway response to growth factor negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 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 ubiquitin-dependent protein catabolic process protein K6-linked ubiquitination protein polyubiquitination DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress DNA repair protein K11-linked ubiquitination protein K48-linked ubiquitination RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic 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 regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process protein monoubiquitination	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen endosome membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR043540	E3 ubiquitin-protein ligase RING1/RING2	Family
C	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
C	IPR032443	RAWUL domain	Domain
C	IPR037937	E3 ubiquitin-protein ligase RING2, RAWUL domain	Domain
C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C	IPR001841	Zinc finger, RING-type	Domain
B	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
B	IPR032443	RAWUL domain	Domain
B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B	IPR001841	Zinc finger, RING-type	Domain
A	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: Q99496	astrocytic tumor oligodendroglioma breast carcinoma epilepsy
B	Pharos: P35226	glioblastoma osteosarcoma malignant glioma leukemia, myeloid, accelerated-phase mixed glioma cancer myelodysplastic syndrome giant cell glioblastoma breast carcinoma Disease Exacerbation glioma ovarian cancer dermatomyositis medulloblastoma
A	Pharos: P61077	pancreatic intraductal papillary-mucinous neoplasm pituitary cancer rheumatoid arthritis astrocytic tumor autism spectrum disorder endogenous depression IgA glomerulonephritis malignant ependymoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell myeloma attention deficit hyperactivity disorder, inattentive type Down syndrome esophageal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm pituitary cancer rheumatoid arthritis astrocytic tumor autism spectrum disorder endogenous depression IgA glomerulonephritis malignant ependymoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell myeloma attention deficit hyperactivity disorder, inattentive type Down syndrome esophageal adenocarcinoma juvenile dermatomyositis medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma Pick disease progressive supranuclear palsy atypical teratoid rhabdoid tumor Emery-Dreifuss muscular dystrophy glioblastoma large cell medulloblastoma myopathy ovarian cancer

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.