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- PDB-1vpf: STRUCTURE OF HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR -

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Basic information

Entry
Database: PDB / ID: 1vpf
TitleSTRUCTURE OF HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR
ComponentsVASCULAR ENDOTHELIAL GROWTH FACTOR
KeywordsGROWTH FACTOR / CYSTINE KNOT / ANGIOGENESIS / VASCULOGENESIS
Function / homology
Function and homology information


basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor 1 binding ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor 1 binding / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor binding / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / 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 / lung vasculature development / cardiac vascular smooth muscle cell development / lymphangiogenesis / eye photoreceptor cell development / endothelial cell chemotaxis / positive regulation of trophoblast cell migration / positive regulation of epithelial tube formation / vascular endothelial growth factor receptor-2 signaling pathway / motor neuron migration / 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 / regulation of hematopoietic progenitor cell differentiation / positive regulation of protein localization to early endosome / 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 / positive regulation of vascular permeability / dopaminergic neuron differentiation / tube formation / commissural neuron axon guidance / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / cardiac muscle cell development / epithelial cell maturation / positive regulation of positive chemotaxis / sprouting angiogenesis / Regulation of gene expression by Hypoxia-inducible Factor / endothelial cell proliferation / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of endothelial cell chemotaxis / artery morphogenesis / positive regulation of p38MAPK cascade / negative regulation of epithelial to mesenchymal transition / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive chemotaxis / positive regulation of neuroblast proliferation / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of fat cell differentiation / positive regulation of sprouting angiogenesis / chemoattractant activity / positive regulation of focal adhesion assembly / outflow tract morphogenesis / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / neuroblast proliferation / mammary gland alveolus development / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / homeostasis of number of cells within a tissue / epithelial cell differentiation / positive regulation of endothelial cell proliferation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell migration
Similarity search - Function
Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family ...Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsMuller, Y.A. / De Vos, A.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Vascular endothelial growth factor: crystal structure and functional mapping of the kinase domain receptor binding site.
Authors: Muller, Y.A. / Li, B. / Christinger, H.W. / Wells, J.A. / Cunningham, B.C. / de Vos, A.M.
#1: Journal: Proteins / Year: 1996
Title: Crystallization of the Receptor Binding Domain of Vascular Endothelial Growth Factor
Authors: Christinger, H.W. / Muller, Y.A. / Berleau, L.T. / Keyt, B.A. / Cunningham, B.C. / Ferrara, N. / De Vos, A.M.
History
DepositionApr 8, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VASCULAR ENDOTHELIAL GROWTH FACTOR
B: VASCULAR ENDOTHELIAL GROWTH FACTOR
C: VASCULAR ENDOTHELIAL GROWTH FACTOR
D: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)47,7954
Polymers47,7954
Non-polymers00
Water3,441191
1
A: VASCULAR ENDOTHELIAL GROWTH FACTOR
B: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)23,8972
Polymers23,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-25 kcal/mol
Surface area10790 Å2
MethodPISA
2
C: VASCULAR ENDOTHELIAL GROWTH FACTOR
D: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)23,8972
Polymers23,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-24 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.190, 59.810, 77.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.998934, 0.046111, 0.0021), (0.046138, 0.996116, 0.075), (0.001366, 0.075017, -0.997181)39.7, -1.6, 17.93
2given(-0.999584, -0.028418, 0.005004), (0.02843, -0.999593, 0.002344), (0.004935, 0.002485, 0.999985)11.6, 5.22, -38.82
3given(0.999837, 0.017115, 0.005777), (0.016532, -0.995875, 0.089215), (0.00728, -0.089105, -0.995996)27.7, 1.15, 57.1

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Components

#1: Protein
VASCULAR ENDOTHELIAL GROWTH FACTOR / VEGF / VASCULAR PERMEABILITY FACTOR / VPF


Mass: 11948.680 Da / Num. of mol.: 4 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P15692
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Details: Christinger, H.W., (1996) Proteins: Struct.,Funct., Genet., 26, 353.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
220 mMTris-HCl1drop
30.4 M1dropNaCl
414 %PEG33501reservoir
520 %isopropanol1reservoir
60.2 Mammonium acetate1reservoir
70.2 M1reservoirCaCl2
80.4 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 17684 / % possible obs: 97 % / Redundancy: 3.6 % / Rsym value: 0.041 / Net I/σ(I): 56.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.2 % / Rsym value: 0.103 / % possible all: 96
Reflection
*PLUS
Rmerge(I) obs: 0.041

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
XDSdata reduction
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: A SOLVENT MASK WAS APPLIED DURING THE FINAL REFINEMENT ROUNDS
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1755 9.9 %IN SMALL SHELLS
Rwork0.205 ---
obs0.205 16942 95.8 %-
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.29 Å20 Å20 Å2
2---32.48 Å20 Å2
3---20.1816 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3044 0 0 191 3235
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.69
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.63
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.71.5
X-RAY DIFFRACTIONx_mcangle_it32
X-RAY DIFFRACTIONx_scbond_it2.32
X-RAY DIFFRACTIONx_scangle_it3.62.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.385 234 9.6 %
Rwork0.363 1423 -
obs--90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.63

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