2M59 | pdb_00002m59

Spatial structure of dimeric VEGFR2 membrane domain in DPC micelles

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF17988	VEGFR-2 Transmembrane domain (VEGFR-2_TMD)	VEGFR-2 Transmembrane domain	This is a transmembrane domain (TMD) of vascular endothelial growth factor receptor 2 which regulates blood vessel homeostasis. Transmembrane signalling by receptor tyrosine kinases (RTKs) requires specific orientation of the intracellular kinase dom ...	This is a transmembrane domain (TMD) of vascular endothelial growth factor receptor 2 which regulates blood vessel homeostasis. Transmembrane signalling by receptor tyrosine kinases (RTKs) requires specific orientation of the intracellular kinase domains in active receptor dimers. Two mutants in VEGFR-2 TMD showed constitutive kinase activity, suggesting that precise TMD orientation is mandatory for kinase activation. Scanning mutagenesis and structural analysis indicated that introducing two polar amino acids in distinct positions of the TMD (G770E/F777E and I771E/L778E mutations) reorients transmembrane helices and leads to stable dimer formation. Therefore, it has been suggested that the transition between the inactive and the active dimeric state of VEGFR-2 implicates alternative dimeric TMD conformations [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Vascular endothelial growth factor receptor 2	molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity collagen receptor activity protein tyrosine kinase collagen receptor activity GPI-linked ephrin receptor activity protein-hormone receptor activity insulin receptor 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 platelet-derived growth factor beta-receptor activity platelet-derived growth factor receptor activity stem cell factor receptor activity cell adhesion molecule binding cadherin binding protein binding brain-derived neurotrophic factor receptor activity neurotrophin receptor activity hepatocyte growth factor receptor activity macrophage colony-stimulating factor receptor activity platelet-derived growth factor alpha-receptor activity growth factor binding vascular endothelial growth factor receptor activity histone H2AXY142 kinase activity histone modifying activity histone kinase activity histone H2AX kinase activity coreceptor activity histone H3Y41 kinase activity histone H3 kinase activity placental growth factor receptor activity insulin-like growth factor receptor activity identical protein binding Hsp90 protein binding heat shock protein binding boss receptor activity epidermal growth factor receptor activity protein-containing complex binding integrin binding signaling receptor binding vascular endothelial growth factor binding fibroblast growth factor receptor activity	multicellular organismal process multicellular organismal-level homeostasis chemical homeostasis homeostatic process multicellular organismal-level chemical homeostasis surfactant homeostasis regulation of cellular process regulation of developmental process cellular developmental process positive regulation of biological process regulation of vasculogenesis regulation of cell differentiation vasculogenesis positive regulation of developmental process multicellular organismal process multicellular organismal-level homeostasis chemical homeostasis homeostatic process multicellular organismal-level chemical homeostasis surfactant homeostasis regulation of cellular process regulation of developmental process cellular developmental process positive regulation of biological process regulation of vasculogenesis regulation of cell differentiation vasculogenesis positive regulation of developmental process multicellular organism development tube morphogenesis positive regulation of cell differentiation cell differentiation anatomical structure development positive regulation of cellular process blood vessel development system development developmental process regulation of biological process blood vessel morphogenesis tube development biological regulation vasculature development circulatory system development anatomical structure morphogenesis cellular process positive regulation of vasculogenesis cellular response to stimulus cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus cell surface receptor protein tyrosine kinase signaling pathway cell communication vascular endothelial growth factor signaling pathway cellular response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus signal transduction response to growth factor enzyme-linked receptor protein signaling pathway regulation of multicellular organismal development animal organ development regulation of bone development skeletal system development regulation of multicellular organismal process bone development regulation of cellular component organization positive regulation of cellular component organization cell-substrate junction assembly positive regulation of cell-substrate junction organization cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly positive regulation of cell-substrate adhesion regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly positive regulation of focal adhesion assembly positive regulation of cellular component biogenesis regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization regulation of focal adhesion assembly regulation of cell-substrate junction assembly hemopoiesis cell development embryo development embryonic hemopoiesis embryonic organ development branching morphogenesis of an epithelial tube angiogenesis epithelial tube morphogenesis epithelium development morphogenesis of an epithelium tissue development branching involved in blood vessel morphogenesis tissue morphogenesis morphogenesis of a branching structure anatomical structure formation involved in morphogenesis morphogenesis of a branching epithelium inorganic ion homeostasis monoatomic ion homeostasis calcium ion homeostasis monoatomic cation homeostasis cell fate commitment positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling positive regulation of mesenchymal cell proliferation cell population proliferation positive regulation of cell population proliferation regulation of mesenchymal cell proliferation regulation of cell population proliferation mesenchymal cell proliferation endothelial cell differentiation endothelium development epithelial cell differentiation cell surface receptor protein serine/threonine kinase signaling pathway regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of BMP signaling pathway BMP signaling pathway cellular response to BMP stimulus regulation of BMP signaling pathway regulation of cellular response to growth factor stimulus positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway response to BMP transforming growth factor beta receptor superfamily signaling pathway heart development endocardium development positive regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of cell migration positive regulation of blood vessel endothelial cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration cell migration cell motility locomotion epithelial cell proliferation positive regulation of autophagy catabolic process macroautophagy autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of macroautophagy metabolic process positive regulation of macroautophagy process utilizing autophagic mechanism regulation of metabolic process positive regulation of organelle organization regulation of anatomical structure morphogenesis mitochondrion organization organelle fission mitochondrial fission regulation of organelle organization organelle organization regulation of mitochondrial fission regulation of mitochondrion organization positive regulation of mitochondrial fission wound healing angiogenesis involved in wound healing vascular wound healing response to stress response to wounding negative regulation of endothelial cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process endothelial cell apoptotic process apoptotic process programmed cell death regulation of endothelial cell apoptotic process regulation of biosynthetic process negative regulation of metabolic process 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 regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of macromolecule metabolic process endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation vascular endothelial growth factor receptor signaling pathway lymph vessel development respiratory tube development lung development respiratory system development lung alveolus development protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process peptidyl-tyrosine modification peptidyl-tyrosine autophosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process peptidyl-tyrosine phosphorylation protein modification process phosphorus metabolic process camera-type eye morphogenesis sensory organ development eye development post-embryonic camera-type eye development visual system development post-embryonic camera-type eye morphogenesis eye morphogenesis post-embryonic eye morphogenesis sensory organ morphogenesis camera-type eye development animal organ morphogenesis post-embryonic development sensory system development cellular response to chemical stimulus response to chemical cellular response to hydrogen sulfide response to hydrogen sulfide regulation of mitochondrial depolarization positive regulation of membrane depolarization positive regulation of mitochondrial depolarization mitochondrial depolarization regulation of membrane depolarization regulation of mitochondrial membrane potential membrane depolarization regulation of biological quality regulation of membrane potential cell migration involved in sprouting angiogenesis sprouting angiogenesis regulation of stem cell proliferation positive regulation of stem cell proliferation stem cell proliferation gonad development reproductive system development reproductive process female gonad development sex differentiation female sex differentiation development of primary female sexual characteristics developmental process involved in reproduction development of primary sexual characteristics reproductive structure development ovarian follicle development vascular endothelial growth factor receptor-2 signaling pathway developmental maturation epithelial cell development anatomical structure maturation epithelial cell maturation cell maturation positive regulation of cell migration involved in sprouting angiogenesis regulation of cell migration involved in sprouting angiogenesis blood vessel endothelial cell differentiation regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process regulation of cell shape cell morphogenesis regulation of cell morphogenesis positive chemotaxis chemotaxis regulation of response to external stimulus positive regulation of positive chemotaxis response to external stimulus regulation of chemotaxis positive regulation of chemotaxis regulation of positive chemotaxis positive regulation of response to external stimulus taxis positive regulation of endothelial cell chemotaxis endothelial cell chemotaxis cell chemotaxis regulation of endothelial cell chemotaxis semaphorin-plexin signaling pathway regulation of vasculature development positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis positive regulation of multicellular organismal process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of protein modification process regulation of phosphate metabolic process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation positive regulation of phosphorus metabolic process regulation of protein metabolic process regulation of phosphorus metabolic process regulation of phosphorylation regulation of hematopoietic progenitor cell differentiation hematopoietic progenitor cell differentiation	protein-containing complex receptor complex membrane-bounded organelle intracellular anatomical structure sorting endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm protein-containing complex receptor complex membrane-bounded organelle intracellular anatomical structure sorting endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle cell periphery plasma membrane membrane membrane microdomain membrane raft extracellular region cell surface external side of plasma membrane side of membrane Golgi apparatus cell junction anchoring junction early endosome nucleus endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001824	Tyrosine-protein kinase, receptor class III, conserved site	Conserved Site
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR003599	Immunoglobulin domain subtype	Domain
A, B	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B	IPR041348	VEGFR-2, transmembrane domain	Domain
A, B	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B	IPR009136	Vascular endothelial growth factor receptor 2 (VEGFR2)	Family
A, B	IPR055229	VEGFR1-3, fifth immunoglobulin-like domain	Domain
A, B	IPR003598	Immunoglobulin subtype 2	Domain
A, B	IPR013098	Immunoglobulin I-set	Domain
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR050122	Receptor Tyrosine Kinase	Family
A, B	IPR055238	VEGFR1-3, N-terminal Ig-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P35968	angiosarcoma capillary infantile hemangioma non-small cell lung carcinoma tubular adenocarcinoma adenocarcinoma Venous Thrombosis schizophrenia temporal lobe epilepsy esophageal cancer uremia cancer multiple epiphyseal dysplasia granular cell carcinoma breast carcinoma osteochondrodysplasia angiosarcoma capillary infantile hemangioma non-small cell lung carcinoma tubular adenocarcinoma adenocarcinoma Venous Thrombosis schizophrenia temporal lobe epilepsy esophageal cancer uremia cancer multiple epiphyseal dysplasia granular cell carcinoma breast carcinoma osteochondrodysplasia colorectal cancer lung adenocarcinoma diabetic kidney disease major depressive disorder spondyloepiphyseal dysplasia tarda, X-linked endometrial carcinoma malignant pancreatic neoplasm thyroid gland follicular carcinoma medullary thyroid gland carcinoma facioscapulohumeral muscular dystrophy gastrointestinal stromal tumor myocardial ischemia hepatocellular carcinoma breast disease hypertensive disorder ovarian cancer pancreatic neoplasm colorectal carcinoma intracerebral hemorrhage renal cell carcinoma coronary artery disease kidney disease cystic fibrosis lung cancer malignant ependymoma sinusitis endometriosis thyroid gland papillary carcinoma Melnick-Needles syndrome ulcerative colitis gastric adenocarcinoma glioblastoma neoplasm of esophagus breast cancer idiopathic pulmonary fibrosis pancreatic intraductal papillary-mucinous carcinoma interstitial lung disease invasive ductal breast carcinoma cribriform carcinoma Schwartz-Jampel syndrome lung disease malignant mesothelioma spondyloepiphyseal dysplasia thymic carcinoma transitional cell carcinoma gastric cancer interstitial cystitis pancreatic intraductal papillary-mucinous neoplasm intestinal disease ischemia reperfusion injury cribriform carcinoma of breast

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Bitopic proteins	Receptor-type kinases	Protein tyrosine kinases

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Vascular Endothelial Growth Factor Receptors	VEGFR2 vascular endothelial growth factor receptor 2 transmembrane dimer

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.