7M4N | pdb_00007m4n

Crystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
C	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	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	ubiquitin_1	e7m4nC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D	ubiquitin_1	e7m4nD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
E	ubiquitin_1	e7m4nE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
F	ubiquitin_1	e7m4nF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF26200	RNF216 Rcat domain (Rcat_RNF216)	RNF216 Rcat domain	This entry represents the Rcat domain in RNF216 and similar proteins. RNF216 proteins are RBR-type E3 ubiquitin ligases that facilitate the transfer of ubiquitin from E2 ubiquitin-conjugating enzymes to target substrates, promoting their ubiquitinati ...	This entry represents the Rcat domain in RNF216 and similar proteins. RNF216 proteins are RBR-type E3 ubiquitin ligases that facilitate the transfer of ubiquitin from E2 ubiquitin-conjugating enzymes to target substrates, promoting their ubiquitination. They play a crucial role in regulating antiviral responses by degrading proteins such as TRAF3, TLR4, and TLR9, thereby modulating NF-kappa-B and IRF3 activation and beta interferon production. Additionally, they are involved in autophagy regulation by targeting BECN1 for degradation, and in synaptic plasticity by mediating ARC ubiquitination. These proteins are essential for spermatogenesis and male fertility, influencing meiosis through PRKACB degradation. They also affect the gonadotropin-releasing hormone pathway by stabilising STAU2, which is necessary for neuronal RNA transport [1-3]. This domain is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain.	Domain
C, D, E, F	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	E3 ubiquitin-protein ligase RNF216	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity	regulation of defense response regulation of response to biotic stimulus regulation of biological process biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus defense response response to other organism biological regulation response to external stimulus response to biotic stimulus regulation of defense response to virus defense response to virus regulation of response to stimulus response to stress regulation of defense response regulation of response to biotic stimulus regulation of biological process biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus defense response response to other organism biological regulation response to external stimulus response to biotic stimulus regulation of defense response to virus defense response to virus regulation of response to stimulus response to stress regulation of response to stress regulation of defense response to virus by host response to external biotic stimulus response to virus multicellular organismal process regulation of cellular process negative regulation of biological process negative regulation of type I interferon production cytokine production negative regulation of cellular process 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 metabolic process 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 metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein K48-linked ubiquitination protein modification by small protein conjugation protein modification by small protein conjugation or removal apoptotic process cell death programmed cell death regulation of interferon-beta production interferon-beta production catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process	membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle clathrin-coated vesicle coated vesicle cytoplasm vesicle cytosol nucleus membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle clathrin-coated vesicle coated vesicle cytoplasm vesicle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, D, E, F	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 proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002867	IBR domain	Domain
A, B	IPR044066	TRIAD supradomain	Domain
A, B	IPR047546	E3 ubiquitin-protein ligase RNF216, Rcat domain	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR047545	E3 ubiquitin-protein ligase RNF216, BRcat domain	Domain
A, B	IPR051628	Linear Ubiquitination-Associated E3 Ligases	Family
A, B	IPR047544	E3 ubiquitin-protein ligase RNF216, RING finger, HC subclass	Domain
C, D, E, F	IPR019954	Ubiquitin conserved site	Conserved Site
C, D, E, F	IPR000626	Ubiquitin-like domain	Domain
C, D, E, F	IPR019956	Ubiquitin domain	Domain
C, D, E, F	IPR050158	Ubiquitin and ubiquitin-like	Family
C, D, E, F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9NWF9	cerebellar ataxia-hypogonadism syndrome Klinefelter syndrome Ataxias, Hereditary ovarian cancer intellectual disability
C, D, E, F	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

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.