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Yorodumi- PDB-1qty: VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF TH... -
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-Basic information
Entry | Database: PDB / ID: 1qty | ||||||
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Title | VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR RECEPTOR / COMPLEX (GROWTH FACTOR-RECEPTOR) / FLT-1 / VEGF RECEPTOR / RECEPTOR TYROSINE KINASE / CYSTINE KNOT / GLYCOPROTEIN / IMMUNOGLOBULIN-LIKE DOMAIN / I-SET / HORMONE-GROWTH FACTOR RECEPTOR complex | ||||||
Function / homology | Function and homology information vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization ...vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / negative regulation of blood-brain barrier permeability / VEGF-activated neuropilin signaling pathway / bone trabecula formation / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lung vasculature development / lymphangiogenesis / eye photoreceptor cell development / Neurophilin interactions with VEGF and VEGFR / positive regulation of trophoblast cell migration / endothelial cell chemotaxis / motor neuron migration / positive regulation of epithelial tube formation / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / regulation of nitric oxide mediated signal transduction / positive regulation of axon extension involved in axon guidance / positive regulation of protein localization to early endosome / vascular wound healing / vascular endothelial growth factor receptor activity / regulation of hematopoietic progenitor cell differentiation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / embryonic morphogenesis / camera-type eye morphogenesis / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / dopaminergic neuron differentiation / negative regulation of epithelial to mesenchymal transition / tube formation / commissural neuron axon guidance / positive regulation of vascular permeability / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / cardiac muscle cell development / epithelial cell maturation / sprouting angiogenesis / negative regulation of vascular endothelial cell proliferation / positive regulation of positive chemotaxis / blood vessel morphogenesis / endothelial cell proliferation / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of p38MAPK cascade / positive regulation of endothelial cell chemotaxis / artery morphogenesis / positive regulation of DNA biosynthetic process / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of neuroblast proliferation / negative regulation of fat cell differentiation / positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / chemoattractant activity / growth factor binding / positive regulation of focal adhesion assembly / monocyte chemotaxis / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / positive regulation of cell division / fibronectin binding / positive regulation of cell adhesion / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / mammary gland alveolus development / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / positive regulation of osteoblast differentiation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT IN COMBINATION WITH MULTI-CRYSTAL AVERAGING / Resolution: 2.7 Å | ||||||
Authors | Wiesmann, C. / de Vos, A.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Solution structure of the VEGF-binding domain of Flt-1: comparison of its free and bound states. Authors: Starovasnik, M.A. / Christinger, H.W. / Wiesmann, C. / Champe, M.A. / de Vos, A.M. / Skelton, N.J. #1: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Crystal Structure at 1.7 A Resolution of Vegf in Complex with Domain 2 of the Flt-1 Receptor Authors: Wiesmann, C. / Fuh, G. / Christinger, H.W. / Eigenbrot, C. / Wells, J.A. / de Vos, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qty.cif.gz | 159.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qty.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/1qty ftp://data.pdbj.org/pub/pdb/validation_reports/qt/1qty | HTTPS FTP |
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-Related structure data
Related structure data | 1qsvC 1qszC 1vpfS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | CHAINS V, W, X, and Y FORM A BIOLOGICALLY ACTIVE COMPLEX. CHAINS R, S, T, and U FORM A BIOLOGICALLY ACTIVE COMPLEX. |
-Components
#1: Protein | Mass: 11948.680 Da / Num. of mol.: 4 / Fragment: RECEPTOR BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P15692 #2: Protein | Mass: 11538.298 Da / Num. of mol.: 4 / Fragment: DOMAIN 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P17948 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.89 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Wiesmann, C., (1997) Cell, 91, 695. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 24, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 24216 / Num. obs: 24098 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.049 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 3 % / Num. unique all: 1544 / Rsym value: 0.311 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT IN COMBINATION WITH MULTI-CRYSTAL AVERAGING Starting model: 1VPF Resolution: 2.7→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R / σ(F): 0.2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 63.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.4 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.383 |