9HXW | pdb_00009hxw

Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (composite map)

External Resource: Annotation

Domain Annotation: SCOP2 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)
B [auth E]	SCOP2B Superfamily	EF-hand	8033438	3001983	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	EF-hand	8033438	3001983	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], E [auth C]	PF00569	Zinc finger, ZZ type (ZZ)	Zinc finger, ZZ type	Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure [2].	Domain
A [auth D], E [auth C]	PF05605	Drought induced 19 protein (Di19), zinc-binding (zf-Di19)	Drought induced 19 protein (Di19), zinc-binding	This family consists of several drought induced 19 (Di19) like proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [1]. This domain is a zinc-binding domain.	Domain
B [auth E], C [auth F]	PF13499	EF-hand domain pair (EF-hand_7)	EF-hand domain pair		Domain
D [auth A], F [auth B]	PF02207	Putative zinc finger in N-recognin (UBR box) (zf-UBR)	Putative zinc finger in N-recognin (UBR box)	-	Family
D [auth A], F [auth B]	PF24079	E3 ubiquitin-protein ligase UBR4-like domain (UBR4)	E3 ubiquitin-protein ligase UBR4-like domain	This domain is found in human E3 ubiquitin-protein ligase UBR4 and similar proteins mainly found in eukaryotes. UBR4 is a component of the N-end rule pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabili ...	This domain is found in human E3 ubiquitin-protein ligase UBR4 and similar proteins mainly found in eukaryotes. UBR4 is a component of the N-end rule pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilising	Domain
D [auth A], F [auth B]	PF19423	E3 ubiquitin-protein ligase UBR4 N-terminal (E3_UBR4_N)	E3 ubiquitin-protein ligase UBR4 N-terminal	This entry represents the N-terminal of E3 ubiquitin-protein ligases UBR4 (POE or PUSHOVER in Drosophila), which are components of the N-rule pathway, identified as noncanonical N-recognins implicated in bulk lysosomal degradation and autophagy. Thes ...	This entry represents the N-terminal of E3 ubiquitin-protein ligases UBR4 (POE or PUSHOVER in Drosophila), which are components of the N-rule pathway, identified as noncanonical N-recognins implicated in bulk lysosomal degradation and autophagy. These are extraordinarily large proteins that recognise and bind to proteins with N-terminal destabilising residues according to the N-end rule leading them to their ubiquitination and degradation. These proteins share a UBR box (Pfam:PF02207) with others E3-ligases UBR box proteins but UBR4 lacks the ubiquitylation domain, suggesting that it may interact with other catalytic proteins [1,2,3].	Domain
D [auth A], F [auth B]	PF13764	E3 ubiquitin-protein ligase UBR4 (E3_UbLigase_R4)	E3 ubiquitin-protein ligase UBR4	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], E [auth C]	E3 ubiquitin-protein ligase KCMF1	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	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 ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process biological regulation 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 ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process biological regulation negative regulation of HRI-mediated signaling protein polyubiquitination protein K63-linked ubiquitination 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 synaptic signaling regulation of biological process signaling cell-cell signaling cell communication response to oxidative stress response to stimulus response to stress proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	cellular anatomical structure extracellular region synapse cell junction intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle cellular anatomical structure extracellular region synapse cell junction intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome vesicle membrane-enclosed lumen ficolin-1-rich granule intracellular organelle lumen organelle lumen ficolin-1-rich granule lumen secretory granule secretory vesicle lytic vacuole vacuole lysosome
B [auth E], C [auth F]	Calmodulin-1	cytoskeletal protein binding titin binding protein binding binding enzyme regulator activity protein phosphatase activator activity enzyme activator activity phosphatase activator activity molecular function activator activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity channel regulator activity ion channel regulator activity cytoskeletal protein binding titin binding protein binding binding enzyme regulator activity protein phosphatase activator activity enzyme activator activity phosphatase activator activity molecular function activator activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity channel regulator activity ion channel regulator activity calcium channel regulator activity transporter regulator activity molecular function inhibitor activity transporter inhibitor activity calcium channel inhibitor activity ion channel inhibitor activity channel inhibitor activity cyclase regulator activity cyclase activator activity adenylate cyclase regulator activity adenylate cyclase activator activity protein serine/threonine kinase activator activity kinase activator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity cation binding ion binding calcium ion binding metal ion binding small molecule binding transmembrane transporter binding kinase binding enzyme binding protein kinase binding calcium-dependent protein binding	organelle localization by membrane tethering localization organelle localization cellular process membrane docking heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation organelle localization by membrane tethering localization organelle localization cellular process membrane docking heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation regulation of multicellular organismal process regulation of biological quality heart contraction blood circulation regulation of heart rate regulation of localization regulation of calcium ion transport negative regulation of ion transmembrane transporter activity regulation of cellular process negative regulation of calcium ion transmembrane transporter activity intracellular calcium ion homeostasis negative regulation of biological process negative regulation of ryanodine-sensitive calcium-release channel activity negative regulation of transport calcium ion transport negative regulation of cation transmembrane transport monoatomic cation homeostasis monoatomic cation transport intracellular monoatomic ion homeostasis regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport establishment of localization maintenance of location transmembrane transport regulation of molecular function release of sequestered calcium ion into cytosol regulation of transmembrane transport chemical homeostasis negative regulation of calcium ion transmembrane transport cellular localization inorganic ion homeostasis transport homeostatic process negative regulation of monoatomic ion transport monoatomic ion transmembrane transport positive regulation of biological process regulation of transmembrane transporter activity calcium ion homeostasis regulation of monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion negative regulation of transmembrane transport metal ion transport maintenance of location in cell regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport positive regulation of sequestering of calcium ion negative regulation of monoatomic ion transmembrane transport negative regulation of release of sequestered calcium ion into cytosol intracellular monoatomic cation homeostasis negative regulation of cellular process monoatomic ion homeostasis monoatomic ion transport intracellular chemical homeostasis regulation of metal ion transport regulation of sequestering of calcium ion positive regulation of cellular process calcium ion transmembrane import into cytosol regulation of transport sequestering of calcium ion negative regulation of transporter activity negative regulation of molecular function negative regulation of calcium ion transport cellular homeostasis regulation of ryanodine-sensitive calcium-release channel activity regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport response to stimulus response to metal ion response to chemical response to calcium ion sarcoplasmic reticulum calcium ion transport release of sequestered calcium ion into cytosol by sarcoplasmic reticulum release of sequestered calcium ion into cytosol by endoplasmic reticulum regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum negative regulation of voltage-gated calcium channel activity regulation of voltage-gated calcium channel activity negative regulation of high voltage-gated calcium channel activity cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation autophagosome membrane docking metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism cellular response to interferon-beta response to peptide response to interferon-beta response to cytokine cellular response to cytokine stimulus regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell division cell cycle regulation of cell cycle cell cycle process cellular response to stimulus cardiac muscle contraction intracellular signal transduction cell communication intracellular signaling cassette signal transduction regulation of cardiac muscle contraction muscle contraction regulation of striated muscle contraction calcium-mediated signaling regulation of muscle contraction signaling regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion striated muscle contraction regulation of cardiac muscle contraction by calcium ion signaling muscle system process regulation of muscle system process mitochondrion-endoplasmic reticulum membrane tethering import into cell presynaptic endocytosis vesicle-mediated transport vesicle-mediated transport in synapse establishment of localization in cell endocytosis cell cycle G2/M phase transition mitotic cell cycle process G2/M transition of mitotic cell cycle cell cycle phase transition mitotic cell cycle mitotic cell cycle phase transition cell communication by electrical coupling involved in cardiac conduction cell communication by electrical coupling regulation of cell communication by electrical coupling involved in cardiac conduction cardiac conduction regulation of cell communication cell communication involved in cardiac conduction regulation of cell communication by electrical coupling export across plasma membrane negative regulation of calcium ion export across plasma membrane regulation of calcium ion export across plasma membrane calcium ion export across plasma membrane export from cell biological process involved in interspecies interaction between organisms immune response response to other organism defense response response to type II interferon defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus calcineurin-mediated signaling developmental process head development animal organ development brain development nervous system development substantia nigra development multicellular organism development central nervous system development midbrain development anatomical structure development neural nucleus development system development positive regulation of cell communication cell surface receptor signaling pathway via STAT positive regulation of signal transduction positive regulation of receptor signaling pathway via STAT regulation of signal transduction positive regulation of receptor signaling pathway via JAK-STAT positive regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT regulation of signaling cell surface receptor signaling pathway regulation of response to stimulus regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT positive regulation of signaling regulation of intracellular signal transduction regulation of calcium-mediated signaling regulation of action potential regulation of cardiac muscle cell action potential action potential cardiac muscle cell action potential regulation of membrane potential G protein-coupled receptor signaling pathway modulation of chemical synaptic transmission long-term synaptic potentiation synaptic signaling regulation of synaptic plasticity trans-synaptic signaling cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling detection of stimulus detection of chemical stimulus detection of calcium ion	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle cell projection intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle cell projection sperm midpiece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection protein-containing complex transmembrane transporter complex membrane membrane protein complex cation channel complex transporter complex calcium channel complex monoatomic ion channel complex axon synapse neuron projection axon terminus presynapse distal axon calyx of Held cell junction neuron projection terminus sarcomere contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex myelin sheath vesicle centrosome microtubule organizing center cytosolic region presynaptic cytosol cell periphery plasma membrane catalytic complex nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen voltage-gated potassium channel complex plasma membrane protein complex potassium channel complex extracellular region polymeric cytoskeletal fiber spindle microtubule microtubule
D [auth A], F [auth B]	E3 ubiquitin-protein ligase UBR4	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 protein binding binding calmodulin binding cation binding transition metal ion 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 protein binding binding calmodulin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	protein polyubiquitination protein branched polyubiquitination 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 regulation of protein stability protein polyubiquitination protein branched polyubiquitination 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 regulation of protein stability biological regulation regulation of biological quality protein stabilization protein K27-linked ubiquitination cellular response to stimulus catabolic process cytoplasm protein quality control response to stimulus proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein cellular response to stress modification-dependent macromolecule catabolic process proteolysis response to stress cellular response to topologically incorrect protein cytoplasm protein quality control by the ubiquitin-proteasome system proteasomal protein catabolic process protein catabolic process modification-dependent protein catabolic process response to topologically incorrect protein ubiquitin-dependent protein catabolic process protein quality control for misfolded or incompletely synthesized proteins negative regulation of HRI-mediated signaling ubiquitin-dependent protein catabolic process via the N-end rule pathway protein K11-linked ubiquitination protein K48-linked ubiquitination response to oxidative stress regulation of cellular process negative regulation of small molecule metabolic process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process negative regulation of biological process lipid biosynthetic process organic acid metabolic process organic acid biosynthetic process negative regulation of lipid biosynthetic process carboxylic acid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process negative regulation of cellular process small molecule metabolic process negative regulation of fatty acid biosynthetic process regulation of biosynthetic process regulation of biological process fatty acid metabolic process negative regulation of fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process negative regulation of metabolic process carboxylic acid metabolic process fatty acid biosynthetic process regulation of ketone metabolic process biosynthetic process negative regulation of biosynthetic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process regulation of lipid biosynthetic process monocarboxylic acid metabolic process regulation of metabolic process negative regulation of lipid metabolic process lipid metabolic process positive regulation of autophagy autophagy positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process process utilizing autophagic mechanism positive regulation of cellular process vesicle organization cellular component organization organelle organization endosome organization cellular component organization or biogenesis endomembrane system organization	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule membrane specific granule centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytosol cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endosome ficolin-1-rich granule membrane ficolin-1-rich granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], E [auth C]	IPR043145	Zinc finger, ZZ-type superfamily	Homologous Superfamily
A [auth D], E [auth C]	IPR013087	Zinc finger C2H2-type	Domain
A [auth D], E [auth C]	IPR008598	Di19, zinc-binding domain	Domain
A [auth D], E [auth C]	IPR050774	KCMF1 and Dystrophin	Family
A [auth D], E [auth C]	IPR000433	Zinc finger, ZZ-type	Domain
B [auth E], C [auth F]	IPR002048	EF-hand domain	Domain
B [auth E], C [auth F]	IPR050230	Calmodulin/Myosin light chain/Troponin C-like	Family
B [auth E], C [auth F]	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
B [auth E], C [auth F]	IPR011992	EF-hand domain pair	Homologous Superfamily
D [auth A], F [auth B]	IPR016024	Armadillo-type fold	Homologous Superfamily
D [auth A], F [auth B]	IPR047509	E3 ubiquitin-protein ligase UBR4-like, UBR-box	Domain
D [auth A], F [auth B]	IPR025704	E3 ubiquitin ligase UBR4, C-terminal	Domain
D [auth A], F [auth B]	IPR045189	E3 ubiquitin ligase UBR4-like	Family
D [auth A], F [auth B]	IPR003126	Zinc finger, UBR-type	Domain
D [auth A], F [auth B]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
D [auth A], F [auth B]	IPR056530	E3 ubiquitin-protein ligase UBR4-like domain	Domain
D [auth A], F [auth B]	IPR045841	E3 ubiquitin-protein ligase UBR4, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth D], E [auth C]	Pharos: Q9P0J7	astrocytic tumor malignant glioma ovarian cancer subependymal giant cell astrocytoma lung cancer malignant pancreatic neoplasm pancreatic ductal adenocarcinoma malignant ependymoma osteosarcoma plasma cell myeloma
B [auth E], C [auth F]	Pharos: P0DP23	long QT syndrome catecholaminergic polymorphic ventricular tachycardia Alzheimer disease long QT syndrome 14 cocaine abuse Weight Gain cannabis dependence cocaine dependence phencyclidine abuse catecholaminergic polymorphic ventricular tachycardia 4 rheumatoid arthritis glioblastoma subependymal giant cell astrocytoma large cell medulloblastoma lung adenocarcinoma long QT syndrome catecholaminergic polymorphic ventricular tachycardia Alzheimer disease long QT syndrome 14 cocaine abuse Weight Gain cannabis dependence cocaine dependence phencyclidine abuse catecholaminergic polymorphic ventricular tachycardia 4 rheumatoid arthritis glioblastoma subependymal giant cell astrocytoma large cell medulloblastoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm astrocytic tumor myopathy osteosarcoma pituitary cancer Crohn disease primitive neuroectodermal tumor familial long QT syndrome schizophrenia lung cancer malignant ependymoma atypical teratoid rhabdoid tumor nasopharyngeal carcinoma ovarian cancer catecholaminergic polymorphic ventricular tachycardia 2 Pick disease plasma cell myeloma exocrine pancreatic carcinoma psoriasis sinusitis hepatocellular carcinoma ulcerative colitis lymphoplasmacytic lymphoma malignant glioma amyotrophic lateral sclerosis medulloblastoma breast cancer oligodendroglioma pilocytic astrocytoma
D [auth A], F [auth B]	Pharos: Q5T4S7	Ataxias, Hereditary tuberculosis hepatocellular carcinoma melanoma intellectual disability 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.