6W9D | pdb_00006w9d

RNF12 RING domain in complex with a Ube2d2~Ub conjugate

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)
I	d6w9di_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6w9df_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6w9dc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6w9dg1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6w9dg2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6w9dd1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6w9dd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6w9da1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6w9da2	Artifacts	Tags	Tags	Tags	C-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)
I	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	UBC-like	8040137	3000570	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	UBC-like	8040137	3000570	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	UBC-like	8040137	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)
I	SBP_bac_1	e6w9dI1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: SBP_bac_1	ECOD (develop294)
F	SBP_bac_1	e6w9dF1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: SBP_bac_1	ECOD (develop294)
C	SBP_bac_1	e6w9dC1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: SBP_bac_1	ECOD (develop294)
H	SBP_bac_1	e6w9dH1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: SBP_bac_1	ECOD (develop294)
E	SBP_bac_1	e6w9dE1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: SBP_bac_1	ECOD (develop294)
B	SBP_bac_1	e6w9dB1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: SBP_bac_1	ECOD (develop294)
G	SBP_bac_1	e6w9dG1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: SBP_bac_1	ECOD (develop294)
D	SBP_bac_1	e6w9dD1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: SBP_bac_1	ECOD (develop294)
A	SBP_bac_1	e6w9dA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: SBP_bac_1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
F	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
H	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
E	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
G	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)
D	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)
A	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
B, E, H	PF13639	Ring finger domain (zf-RING_2)	Ring finger domain		Domain
A, D, G	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, F, I	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding nucleic acid binding	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic 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	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B, E, H	E3 ubiquitin-protein ligase RLIM	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding ubiquitin-like protein ligase activity ubiquitin protein ligase activity	regulation of cellular process 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 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 regulation of cellular process 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 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 biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process protein metabolic process developmental process multicellular organismal process regulation of multicellular organismal development regulation of developmental process cellular developmental process cell development regulation of neurogenesis regulation of cell differentiation nervous system development regulation of cell development regulation of nervous system development multicellular organism development neurogenesis cell differentiation anatomical structure development regulation of multicellular organismal process system development transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II 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 cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis random inactivation of X chromosome heterochromatin formation sex-chromosome dosage compensation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression dosage compensation by inactivation of X chromosome negative regulation of gene expression, epigenetic	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex transcription repressor complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex transcription repressor complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
A, D, G	Ubiquitin-conjugating enzyme E2 D2	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 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 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	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination protein ubiquitination macromolecule modification catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination 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 protein K48-linked ubiquitination protein autoubiquitination	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 nucleus 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 nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I	IPR019954	Ubiquitin conserved site	Conserved Site
C, F, I	IPR000626	Ubiquitin-like domain	Domain
C, F, I	IPR019956	Ubiquitin domain	Domain
C, F, I	IPR050158	Ubiquitin and ubiquitin-like	Family
C, F, I	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, E, H	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B, E, H	IPR058896	E3 ubiquitin-protein ligase RNF6/12, N-terminal domain	Domain
B, E, H	IPR051834	RING finger E3 ubiquitin-protein ligase	Family
B, E, H	IPR001841	Zinc finger, RING-type	Domain
A, D, G	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A, D, G	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A, D, G	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F, I	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer
B, E, H	Pharos: Q9NVW2	intellectual disability, X-linked 61 prostate cancer intellectual disability diabetes mellitus Mental Retardation, X-Linked 1 pancreatic ductal adenocarcinoma tuberculosis glioblastoma malignant glioma non-syndromic X-linked intellectual disability ulcerative colitis malignant pancreatic neoplasm ovarian cancer
A, D, G	Pharos: P62837	astrocytic tumor esophageal squamous cell carcinoma malignant ependymoma osteosarcoma atypical teratoid rhabdoid tumor glioblastoma malignant glioma ovarian cancer breast cancer large cell medulloblastoma malignant mesothelioma plasma cell myeloma

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.