3M7F | pdb_00003m7f

Crystal structure of the Nedd4 C2/Grb10 SH2 complex

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
Membrane Protein Annotation: OPM

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3m7fa_	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	PLC-like (P variant)	8086444	4002218	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8086445	3000965	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SH2	e3m7fA1	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2	ECOD (1.6)
B	C2_1	e3m7fB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: C2 domain (From Topology)	T: C2 domain	F: C2_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
B	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00017	SH2 domain (SH2)	SH2 domain		Domain
B	PF00168	C2 domain (C2)	C2 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Growth factor receptor-bound protein 10	protein binding binding signaling receptor binding insulin receptor binding phosphoprotein binding phosphotyrosine residue binding protein phosphorylated amino acid binding protein-macromolecule adaptor activity molecular adaptor activity signaling receptor complex adaptor activity signaling adaptor activity	cellular response to stimulus regulation of cellular process response to stimulus negative regulation of signaling 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 signal transduction Wnt signaling pathway regulation of signaling cellular response to stimulus regulation of cellular process response to stimulus negative regulation of signaling 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 signal transduction Wnt signaling pathway regulation of signaling regulation of biological process cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus biological regulation negative regulation of signal transduction regulation of response to stimulus regulation of cell communication cellular process muscle cell migration vascular associated smooth muscle cell migration cell migration cell motility smooth muscle cell migration intracellular signal transduction intracellular signaling cassette MAPK cascade ERK1 and ERK2 cascade positive regulation of cell communication cellular response to growth factor stimulus positive regulation of signal transduction positive regulation of biological process cell surface receptor protein tyrosine kinase signaling pathway regulation of vascular endothelial growth factor receptor signaling pathway positive regulation of response to stimulus cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway positive regulation of cellular process response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway positive regulation of vascular endothelial growth factor receptor signaling pathway response to growth factor positive regulation of signaling insulin-like growth factor receptor signaling pathway cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway regulation of cellular response to insulin stimulus response to hormone cellular response to hormone stimulus regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus negative regulation of cellular response to insulin stimulus negative regulation of insulin receptor signaling pathway response to chemical response to insulin cellular response to insulin stimulus phosphorylation negative regulation of metabolic process negative regulation of phosphate metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of phosphorus metabolic process regulation of phosphorus metabolic process metabolic process regulation of phosphorylation negative regulation of phosphorylation phosphorus metabolic process regulation of metabolic process regulation of glycogen biosynthetic process negative regulation of glycogen biosynthetic process glucan biosynthetic process energy derivation by oxidation of organic compounds regulation of glucan biosynthetic process regulation of generation of precursor metabolites and energy regulation of polysaccharide metabolic process regulation of primary metabolic process polysaccharide metabolic process glucan metabolic process regulation of carbohydrate metabolic process negative regulation of carbohydrate metabolic process negative regulation of glycogen metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process glycogen metabolic process primary metabolic process generation of precursor metabolites and energy regulation of macromolecule metabolic process glycogen biosynthetic process macromolecule biosynthetic process biosynthetic process negative regulation of biosynthetic process regulation of polysaccharide biosynthetic process negative regulation of macromolecule biosynthetic process energy reserve metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of carbohydrate biosynthetic process regulation of glycogen metabolic process multicellular organismal process homeostatic process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process regulation of multicellular organismal process gene expression regulation of localization hexose transmembrane transport D-glucose import transport carbohydrate transport negative regulation of transport negative regulation of transmembrane transport localization negative regulation of D-glucose import regulation of D-glucose import regulation of transport negative regulation of D-glucose transmembrane transport establishment of localization transmembrane transport regulation of transmembrane transport D-glucose transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex
B	E3 ubiquitin-protein ligase NEDD4	monoatomic cation transmembrane transporter activity channel regulator activity monoatomic ion channel activity sodium channel activity molecular function inhibitor activity passive transmembrane transporter activity transporter inhibitor activity inorganic molecular entity transmembrane transporter activity molecular function regulator activity inorganic cation transmembrane transporter activity sodium channel regulator activity transporter activity channel inhibitor activity ion channel regulator activity monoatomic cation transmembrane transporter activity channel regulator activity monoatomic ion channel activity sodium channel activity molecular function inhibitor activity passive transmembrane transporter activity transporter inhibitor activity inorganic molecular entity transmembrane transporter activity molecular function regulator activity inorganic cation transmembrane transporter activity sodium channel regulator activity transporter activity channel inhibitor activity ion channel regulator activity ion channel inhibitor activity sodium ion transmembrane transporter activity monoatomic cation channel activity sodium channel inhibitor activity channel activity monoatomic ion transmembrane transporter activity transporter regulator activity metal ion transmembrane transporter activity transmembrane transporter activity phosphoprotein binding protein binding binding phosphoserine residue binding protein phosphorylated amino acid binding ionotropic glutamate receptor binding signaling receptor binding glutamate receptor binding phosphothreonine residue 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 proline-rich region binding	response to stimulus immune response immune system process adaptive immune response cellular component organization cell junction organization neuromuscular junction development cellular process synapse organization cellular component organization or biogenesis regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process response to stimulus immune response immune system process adaptive immune response cellular component organization cell junction organization neuromuscular junction development cellular process synapse organization cellular component organization or biogenesis regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process regulation of cellular component organization regulation of synapse organization regulation of synapse structure or activity regulation of biological quality 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 regulation of localization transport regulation of transport regulation of monoatomic ion transport negative regulation of monoatomic ion transport negative regulation of biological process negative regulation of transport regulation of sodium ion transport establishment of localization metal ion transport localization monoatomic ion transport negative regulation of sodium ion transport monoatomic cation transport regulation of metal ion transport sodium ion transport cellular response to stimulus cellular response to growth factor stimulus signaling negative regulation of signaling regulation of signal transduction negative regulation of cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication regulation of vascular endothelial growth factor receptor signaling pathway cellular response to endogenous stimulus negative regulation of vascular endothelial growth factor receptor signaling pathway negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction vascular endothelial growth factor receptor signaling pathway regulation of response to stimulus regulation of cell communication response to growth factor cellular localization establishment of localization in cell multicellular organismal process T cell activation cell activation lymphocyte activation leukocyte activation proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process protein polyubiquitination protein K63-linked ubiquitination developmental process multicellular organism development anatomical structure development nervous system development system development regulation of neuron projection development regulation of developmental process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation dendrite development neuron projection morphogenesis regulation of dendrite morphogenesis cell differentiation regulation of anatomical structure morphogenesis plasma membrane bounded cell projection organization regulation of cell projection organization dendrite morphogenesis cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis regulation of dendrite development neuron development regulation of plasma membrane bounded cell projection organization RNA 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 transcription by RNA polymerase II 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 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 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 regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process protein monoubiquitination blood vessel morphogenesis tube development vasculature development circulatory system development tube morphogenesis blood vessel development heart development animal organ development mesenchyme development tissue development endocardial cushion development heart morphogenesis outflow tract morphogenesis animal organ morphogenesis	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane synapse cell junction glutamatergic synapse protein-containing complex ubiquitin ligase complex catalytic complex transferase complex cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane synapse cell junction glutamatergic synapse protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle cytosolic region postsynapse postsynaptic cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001849	Pleckstrin homology domain	Domain
A	IPR039664	GRB/APBB1IP	Family
A	IPR015042	BPS (Between PH and SH2) domain	Domain
A	IPR036860	SH2 domain superfamily	Homologous Superfamily
A	IPR039665	APBB1IP, PH domain	Domain
A	IPR000980	SH2 domain	Domain
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR035037	Grb10, SH2	Domain
A	IPR000159	Ras-associating domain	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR035983	HECT, E3 ligase catalytic domain	Homologous Superfamily
B	IPR036020	WW domain superfamily	Homologous Superfamily
B	IPR000008	C2 domain	Domain
B	IPR050409	E3 ubiquitin-protein ligase	Family
B	IPR000569	HECT domain	Domain
B	IPR024928	E3 ubiquitin-protein ligase, SMURF1 type	Family
B	IPR035892	C2 domain superfamily	Homologous Superfamily
B	IPR001202	WW domain	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
B	OPM				C2 domain

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.