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- PDB-3v2a: VEGFR-2/VEGF-A COMPLEX STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 3v2a
TitleVEGFR-2/VEGF-A COMPLEX STRUCTURE
Components
  • Vascular endothelial growth factor A
  • Vascular endothelial growth factor receptor 2
KeywordsHORMONE/SIGNALING PROTEIN / IG-HOMOLOGY DOMAIN / VEGFR-2 / GROWTH FACTOR RECEPTOR / VEGF LIGAND / HORMONE-SIGNALING PROTEIN COMPLEX / ANGIOGENESIS / MEMBRANE / VEGF-A
Function / homology
Function and homology information


Signaling by VEGF / basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / positive regulation of nitric oxide-cGMP mediated signal transduction / : / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor 1 binding / negative regulation of adherens junction organization / primitive erythrocyte differentiation ...Signaling by VEGF / basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / positive regulation of nitric oxide-cGMP mediated signal transduction / : / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor 1 binding / negative regulation of adherens junction organization / primitive erythrocyte differentiation / positive regulation of mast cell chemotaxis / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / post-embryonic camera-type eye development / lymph vessel morphogenesis / negative regulation of blood-brain barrier permeability / VEGF-activated neuropilin signaling pathway / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / eye photoreceptor cell development / motor neuron migration / cellular response to hydrogen sulfide / endothelium development / coronary vein morphogenesis / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / cardiac vascular smooth muscle cell development / Neuropilin interactions with VEGF and VEGFR / endocardium development / vascular endothelial growth factor binding / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor-2 signaling pathway / endothelial cell differentiation / vascular endothelial growth factor receptor activity / positive regulation of axon extension involved in axon guidance / endothelial cell chemotaxis / positive regulation of protein localization to early endosome / positive regulation of trophoblast cell migration / surfactant homeostasis / positive regulation of protein autophosphorylation / camera-type eye morphogenesis / positive regulation of vasculogenesis / vascular wound healing / induction of positive chemotaxis / retinal ganglion cell axon guidance / dopaminergic neuron differentiation / positive regulation of epithelial tube formation / transmembrane receptor protein tyrosine kinase activator activity / neuropilin binding / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / tube formation / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of leukocyte migration / cell migration involved in sprouting angiogenesis / vascular endothelial growth factor receptor 2 binding / positive regulation of BMP signaling pathway / positive regulation of vascular permeability / commissural neuron axon guidance / positive regulation of vascular endothelial growth factor signaling pathway / artery morphogenesis / cardiac muscle cell development / branching involved in blood vessel morphogenesis / embryonic hemopoiesis / positive regulation of blood vessel branching / sprouting angiogenesis / platelet-derived growth factor receptor binding / extracellular matrix binding / anchoring junction / positive regulation of positive chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of neuroblast proliferation / positive regulation of endothelial cell chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / negative regulation of epithelial to mesenchymal transition / vascular endothelial growth factor signaling pathway / positive regulation of mitochondrial fission / mammary gland alveolus development / growth factor binding / sorting endosome / positive chemotaxis / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / chemoattractant activity / positive regulation of mitochondrial depolarization / mesoderm development / macrophage differentiation / fibronectin binding / positive regulation of macroautophagy / monocyte differentiation / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / semaphorin-plexin signaling pathway / regulation of MAPK cascade / vasculogenesis / lung development / positive regulation of receptor internalization / heart morphogenesis / positive regulation of focal adhesion assembly / negative regulation of endothelial cell apoptotic process
Similarity search - Function
Vascular endothelial growth factor A, long form-like domain / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain ...Vascular endothelial growth factor A, long form-like domain / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR-1-like, immunoglobulin-like 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 / : / VEGFR1-3, N-terminal Ig-like domain / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin domain / Cystine-knot cytokine / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form / Vascular endothelial growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.204 Å
AuthorsBrozzo, M.S. / Leppanen, V.-M. / Winkler, F.K. / Ballmer-Hofer, K.
CitationJournal: Blood / Year: 2012
Title: Thermodynamic and structural description of allosterically regulated VEGFR-2 dimerization.
Authors: Brozzo, M.S. / Bjelic, S. / Kisko, K. / Schleier, T. / Leppanen, V.M. / Alitalo, K. / Winkler, F.K. / Ballmer-Hofer, K.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Vascular endothelial growth factor receptor 2
A: Vascular endothelial growth factor A


Theoretical massNumber of molelcules
Total (without water)102,1092
Polymers102,1092
Non-polymers00
Water00
1
R: Vascular endothelial growth factor receptor 2
A: Vascular endothelial growth factor A

R: Vascular endothelial growth factor receptor 2
A: Vascular endothelial growth factor A


Theoretical massNumber of molelcules
Total (without water)204,2184
Polymers204,2184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area6960 Å2
ΔGint-57 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.969, 80.969, 332.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Detailsthe asymmetric unit contains one copy of each component of the complex

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Components

#1: Protein Vascular endothelial growth factor receptor 2 / VEGFR-2 / Fetal liver kinase 1 / FLK-1 / Kinase insert domain receptor / KDR / Protein-tyrosine ...VEGFR-2 / Fetal liver kinase 1 / FLK-1 / Kinase insert domain receptor / KDR / Protein-tyrosine kinase receptor flk-1


Mass: 86566.461 Da / Num. of mol.: 1 / Fragment: UNP residues 1-764
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLK1, KDR, VEGFR2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21
References: UniProt: P35968, receptor protein-tyrosine kinase
#2: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 15542.596 Da / Num. of mol.: 1 / Fragment: UNP residues 27-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGF, VEGF-A, VEGFA / Production host: Pichia pastoris (fungus) / References: UniProt: P15692
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M NaCl, 1.6 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED EXIT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.2→68.608 Å / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 2.1 %
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.25 / Rsym value: 0.76 / % possible all: 94.1

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VEGF-E and VEGFR-2 VEGF-C complex structure

Resolution: 3.204→68.608 Å / SU ML: 0.35 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3005 540 4.78 %random
Rwork0.2444 ---
obs0.2471 11298 98.68 %-
all-0 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 112.925 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.1574 Å20 Å2-0 Å2
2--8.1574 Å2-0 Å2
3----21.5589 Å2
Refinement stepCycle: LAST / Resolution: 3.204→68.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 0 0 2114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042167
X-RAY DIFFRACTIONf_angle_d0.8342946
X-RAY DIFFRACTIONf_dihedral_angle_d14.89754
X-RAY DIFFRACTIONf_chiral_restr0.056341
X-RAY DIFFRACTIONf_plane_restr0.003380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2041-3.52650.39711300.32352607X-RAY DIFFRACTION99
3.5265-4.03670.32751410.2572624X-RAY DIFFRACTION99
4.0367-5.08560.25441360.18942686X-RAY DIFFRACTION99
5.0856-68.62390.30111330.25852841X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0427-0.0233-0.03840.1836-0.07910.1535-0.0981-0.0134-0.2184-0.336-0.1846-0.03650.2041-0.319-0.43830.9326-0.598-0.02550.3940.08190.4825.9981-18.666219.6487
20.03690.0018-0.08150.0639-0.00660.20210.0945-0.0950.25810.360.0455-0.1784-0.2762-0.18970.10151.46620.0774-0.07550.13390.06160.67933.799312.389911.2766
30.17650.05940.16580.01830.05780.1397-0.19640.13380.1154-0.0950.0872-0.30910.3873-0.0083-0.00241.39420.13470.17610.4750.12420.986954.3078-24.51065.3266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain R and resseq 132:219
3X-RAY DIFFRACTION3chain R and resseq 220:329

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