3IXS | pdb_00003ixs

Ring1B C-terminal domain/RYBP C-terminal domain 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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K	SCOP2B Superfamily	Ubiquitin-like	8055976	3000157	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ubiquitin-like	8055976	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8055976	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8055976	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8055976	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8055976	3000157	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Yaf2/RYBP C-terminal binding motif-like	8102967	3002774	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Yaf2/RYBP C-terminal binding motif-like	8102967	3002774	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Yaf2/RYBP C-terminal binding motif-like	8102967	3002774	SCOP2B (2022-06-29)
F	SCOP2 Family	Yaf2/RYBP C-terminal binding motif-like	8046650	4005214	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Yaf2/RYBP C-terminal binding motif-like	8102967	3002774	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Yaf2/RYBP C-terminal binding motif-like	8102967	3002774	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Yaf2/RYBP C-terminal binding motif-like	8102967	3002774	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)
K	RAWUL	e3ixsK1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RAWUL	ECOD (1.6)
I	RAWUL	e3ixsI1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RAWUL	ECOD (1.6)
G	RAWUL	e3ixsG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RAWUL	ECOD (1.6)
E	RAWUL	e3ixsE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RAWUL	ECOD (1.6)
C	RAWUL	e3ixsC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RAWUL	ECOD (1.6)
A	RAWUL	e3ixsA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RAWUL	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
I	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
G	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF16207	RAWUL domain RING finger- and WD40-associated ubiquitin-like (RAWUL)	RAWUL domain RING finger- and WD40-associated ubiquitin-like	The RAWUL domain is found at the C-terminus of poly-comb group RING finger proteins. It is a ubiquitin-like domain [1]. RAWUL binds directly to PUFD, a domain on BCOR proteins (BCL6 corepressor). BCOR has emerged as an important player in developm ...	The RAWUL domain is found at the C-terminus of poly-comb group RING finger proteins. It is a ubiquitin-like domain [1]. RAWUL binds directly to PUFD, a domain on BCOR proteins (BCL6 corepressor). BCOR has emerged as an important player in development and health [2].	Domain
B, D, F, H, J B, D, F, H, J, L	PF17219	Yaf2/RYBP C-terminal binding motif (YAF2_RYBP)	Yaf2/RYBP C-terminal binding motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K	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 regulation of cellular process negative regulation of DNA-binding transcription factor activity 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 regulation of cellular process negative regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process negative regulation of molecular function biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process 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 epigenetic regulation of gene expression cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis 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 negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process 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, D, F, H, J B, D, F, H, J, L	RING1 and YY1-binding protein	DNA binding binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process apoptotic process cell death programmed cell death positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process negative regulation of biological process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis catabolic process negative regulation of proteolysis negative regulation of proteolysis involved in protein catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process negative regulation of protein catabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process proteolysis protein metabolic process negative regulation of protein metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein 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 negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic 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 cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm 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 membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR043540	E3 ubiquitin-protein ligase RING1/RING2	Family
A, C, E, G, I A, C, E, G, I, K	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, C, E, G, I A, C, E, G, I, K	IPR032443	RAWUL domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR037937	E3 ubiquitin-protein ligase RING2, RAWUL domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR001841	Zinc finger, RING-type	Domain
B, D, F, H, J B, D, F, H, J, L	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR039958	RING1 and YY1-binding protein/YY1-associated factor 2	Family
B, D, F, H, J B, D, F, H, J, L	IPR033774	Yaf2/RYBP C-terminal binding motif	Conserved Site
B, D, F, H, J B, D, F, H, J, L	IPR001876	Zinc finger, RanBP2-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K	Pharos: Q99496	astrocytic tumor oligodendroglioma breast carcinoma epilepsy
B, D, F, H, J B, D, F, H, J, L	Pharos: Q8N488	psoriasis allergic rhinitis dermatomyositis large cell medulloblastoma malignant glioma myopathy ovarian cancer pilocytic astrocytoma spina bifida astrocytic tumor glioblastoma lung cancer malignant pancreatic neoplasm oligodendroglioma pancreatic ductal adenocarcinoma psoriasis allergic rhinitis dermatomyositis large cell medulloblastoma malignant glioma myopathy ovarian cancer pilocytic astrocytoma spina bifida astrocytic tumor glioblastoma lung cancer malignant pancreatic neoplasm oligodendroglioma pancreatic ductal adenocarcinoma plasma cell myeloma tuberculosis atypical teratoid rhabdoid tumor juvenile dermatomyositis malignant ependymoma medulloblastoma osteosarcoma Pick 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.