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- PDB-6d3o: Crystal Structure of Vascular Endothelial Growth Factor (VEGF8-10... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d3o | ||||||||||||||||||
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Title | Crystal Structure of Vascular Endothelial Growth Factor (VEGF8-109) with HH4, an alpha/beta-Peptide with Irregular Secondary Structure | ||||||||||||||||||
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![]() | PROTEIN BINDING / alpha/beta-peptide / VEGF | ||||||||||||||||||
Function / homology | ![]() basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / 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 ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / 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 / 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 / endothelial cell chemotaxis / motor neuron migration / positive regulation of trophoblast cell 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 / vascular wound healing / positive regulation of protein localization to early endosome / 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 / 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 / tube formation / positive regulation of vascular permeability / dopaminergic neuron differentiation / commissural neuron axon guidance / negative regulation of epithelial to mesenchymal transition / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / cardiac muscle cell development / epithelial cell maturation / sprouting angiogenesis / positive regulation of positive chemotaxis / 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 / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / chemoattractant activity / outflow tract morphogenesis / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of cell adhesion / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / vasculogenesis / positive regulation of osteoblast differentiation / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / homeostasis of number of cells within a tissue / positive regulation of protein autophosphorylation / positive regulation of endothelial cell proliferation / epithelial cell differentiation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors Similarity search - Function | ||||||||||||||||||
Biological species | ![]() synthetic construct (others) | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Thomas, N.C. / Forest, K.T. / Gellman, S.H. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: High-Resolution Structures for a Complex Between a Non-Helical Foldamer and VEGF Authors: Thomas, N.C. / London, H.S. / Forest, K.T. / Gellman, S.H. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.2 KB | Display | ![]() |
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PDB format | ![]() | 74.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.5 KB | Display | ![]() |
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Full document | ![]() | 458.4 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vpfS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 13 - 106 / Label seq-ID: 6 - 99
NCS oper:
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Components
#1: Protein | Mass: 11862.497 Da / Num. of mol.: 1 / Fragment: residues 34-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 11948.680 Da / Num. of mol.: 1 / Fragment: residues 34-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Protein/peptide | Mass: 1992.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 7198 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 66.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.047 / Rrim(I) all: 0.156 / Net I/σ(I): 13 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1029 / CC1/2: 0.67 / Rpim(I) all: 0.443 / Rrim(I) all: 1.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VPF Resolution: 3.1→33.29 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.877 / SU B: 39.682 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 159.77 Å2 / Biso mean: 77.405 Å2 / Biso min: 51.33 Å2
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Refinement step | Cycle: final / Resolution: 3.1→33.29 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2321 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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