9G09 | pdb_00009g09

Structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF20173	RZ type zinc finger domain (ZnF_RZ-type)	RZ type zinc finger domain	This entry represents the RZ type zinc finger domain, found in NFX1-type zinc finger-containing protein 1 (ZNFX1) and E3 ubiquitin-protein ligase RNF213 from humans. It contains two conserved histidine residues and four conserved cysteine residues in ...	This entry represents the RZ type zinc finger domain, found in NFX1-type zinc finger-containing protein 1 (ZNFX1) and E3 ubiquitin-protein ligase RNF213 from humans. It contains two conserved histidine residues and four conserved cysteine residues in a CHC3H motif. It can bind divalent transition metals, with a preference for Zn2+. ZNFX1 is an RNA-binding protein that initiates the antiviral response and is required to restrict the replication of RNA viruses [1,2]. RNF213 is a giant E3 ubiquitin ligase that can catalyse ubiquitination of both proteins and lipids, which is involved in various processes, such as lipid metabolism, angiogenesis and cell-autonomous immunity. It functions as a key immune sensor by catalysing ubiquitination of the lipid A moiety of bacterial LPS via its RZ-type zinc-finger and restricts the proliferation of cytosolic bacteria [3,4]. RNF213 is a major susceptibility factor of Moyamoya disease [5].	Domain
B [auth A]	PF00097	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4)	Zinc finger, C3HC4 type (RING finger)	The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [1]. Many protein ...	The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [1]. Many proteins containing a RING finger play a key role in the ubiquitination pathway [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	E3 ubiquitin-protein ligase IpaH2.5	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 toxin activity	primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular 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	cellular anatomical structure extracellular region host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region other organism part
B [auth A]	E3 ubiquitin-protein ligase RNF213	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 binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate 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 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 pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides ATP-dependent activity cation binding transition metal ion binding zinc ion binding metal ion binding	regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process blood vessel morphogenesis tube development regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development lipid modification by small protein conjugation lipid ubiquitination lipid modification protein autoubiquitination protein ubiquitination macromolecule modification 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 sprouting angiogenesis defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus catabolic process macroautophagy autophagy xenophagy defense response to other organism process utilizing autophagic mechanism immune system process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process protein polyubiquitination protein K63-linked ubiquitination organelle assembly lipid storage membraneless organelle assembly lipid droplet formation cellular component organization cellular component biogenesis organelle organization cellular component assembly lipid droplet organization nutrient storage cellular component organization or biogenesis cellular response to stimulus signaling negative regulation of signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process non-canonical Wnt signaling pathway signal transduction Wnt signaling pathway regulation of signaling regulation of Wnt signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of non-canonical Wnt signaling pathway negative regulation of non-canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane cytoplasm cytosol lipid droplet

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR051071	Leucine-rich repeat-containing bacterial E3 ubiquitin ligases	Family
A [auth B]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A [auth B]	IPR001611	Leucine-rich repeat	Repeat
A [auth B]	IPR032674	LRR-containing bacterial E3 ligase, N-terminal	Domain
A [auth B]	IPR029487	Novel E3 ligase domain	Domain
B [auth A]	IPR003593	AAA+ ATPase domain	Domain
B [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth A]	IPR018957	Zinc finger, C3HC4 RING-type	Domain
B [auth A]	IPR031248	E3 ubiquitin-protein ligase RNF213	Family
B [auth A]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B [auth A]	IPR046439	Zinc finger, RZ-type	Domain
B [auth A]	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A]	Pharos: Q63HN8	Moyamoya disease Moyamoya disease 2 medulloblastoma moyamoya disease 1 myopathy ovarian cancer acute myeloid leukemia pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor pilocytic astrocytoma cancer psoriasis cystic fibrosis subependymal giant cell astrocytoma interstitial cystitis Moyamoya disease Moyamoya disease 2 medulloblastoma moyamoya disease 1 myopathy ovarian cancer acute myeloid leukemia pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor pilocytic astrocytoma cancer psoriasis cystic fibrosis subependymal giant cell astrocytoma interstitial cystitis lung adenocarcinoma malignant glioma migraine disorder oligodendroglioma pancreatic ductal adenocarcinoma astrocytic tumor pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer pituitary cancer cerebrovascular disorder sinusitis gastric carcinoma tuberculosis invasive ductal breast carcinoma lung carcinoma malignant pancreatic neoplasm multiple sclerosis osteosarcoma pancreatic intraductal papillary-mucinous carcinoma atopic eczema Pick disease breast carcinoma primitive neuroectodermal tumor Crohn disease Sjogren syndrome glioblastoma ulcerative colitis juvenile dermatomyositis malignant ependymoma

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.