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- PDB-3v6b: VEGFR-2/VEGF-E complex structure -

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Basic information

Entry
Database: PDB / ID: 3v6b
TitleVEGFR-2/VEGF-E complex structure
Components
  • VEGF-E
  • Vascular endothelial growth factor receptor 2
KeywordsHORMONE/SIGNALING PROTEIN / Ig-homology domain / VEGFR-2 / growth factor receptor / VEGF ligand / ANGIOGENESIS / MEMBRANE / VEGF-E / Orf virus / HORMONE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


vascular endothelial growth factor receptor binding / blood vessel endothelial cell differentiation / cellular response to hydrogen sulfide / positive regulation of mast cell chemotaxis / regulation of bone development / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / vascular endothelial growth factor binding / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization ...vascular endothelial growth factor receptor binding / blood vessel endothelial cell differentiation / cellular response to hydrogen sulfide / positive regulation of mast cell chemotaxis / regulation of bone development / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / vascular endothelial growth factor binding / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / endothelium development / endocardium development / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / vascular endothelial growth factor receptor activity / post-embryonic camera-type eye morphogenesis / endothelial cell differentiation / positive regulation of vasculogenesis / mesenchymal cell proliferation / lymph vessel development / induction of positive chemotaxis / positive regulation of BMP signaling pathway / surfactant homeostasis / cell migration involved in sprouting angiogenesis / epithelial cell maturation / anchoring junction / sprouting angiogenesis / positive regulation of positive chemotaxis / embryonic hemopoiesis / vascular endothelial growth factor signaling pathway / positive regulation of mesenchymal cell proliferation / positive regulation of endothelial cell chemotaxis / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of mitochondrial fission / positive regulation of mitochondrial depolarization / lung alveolus development / positive regulation of stem cell proliferation / chemoattractant activity / positive regulation of nitric-oxide synthase biosynthetic process / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / regulation of MAPK cascade / semaphorin-plexin signaling pathway / : / positive regulation of macroautophagy / positive regulation of cell division / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / cell fate commitment / calcium ion homeostasis / vasculogenesis / Integrin cell surface interactions / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / negative regulation of endothelial cell apoptotic process / peptidyl-tyrosine autophosphorylation / ovarian follicle development / positive regulation of endothelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of endothelial cell migration / transmembrane receptor protein tyrosine kinase activity / VEGFR2 mediated cell proliferation / epithelial cell proliferation / stem cell proliferation / growth factor activity / Hsp90 protein binding / receptor protein-tyrosine kinase / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / cell migration / integrin binding / cell junction / regulation of cell shape / protein tyrosine kinase activity / angiogenesis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / early endosome / receptor complex / response to hypoxia / endosome / positive regulation of cell migration / cadherin binding / positive regulation of protein phosphorylation / membrane raft / external side of plasma membrane / negative regulation of gene expression / positive regulation of cell population proliferation / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular region / ATP binding
Similarity search - Function
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 / 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 receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-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 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / 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 / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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 receptor 2 / Vascular endothelial growth factor homolog / VEGF
Similarity search - Component
Biological speciesOrf virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.205 Å
AuthorsBrozzo, M.S. / Leppanen, V.-M. / Winkler, F.K. / Kisko, 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 19, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VEGF-E
R: Vascular endothelial growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)63,1992
Polymers63,1992
Non-polymers00
Water00
1
A: VEGF-E
R: Vascular endothelial growth factor receptor 2

A: VEGF-E
R: Vascular endothelial growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)126,3974
Polymers126,3974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area6940 Å2
ΔGint-46 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.879, 79.879, 340.044
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein VEGF-E


Mass: 15504.567 Da / Num. of mol.: 1 / Fragment: VEGF-E, UNP residues 21-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orf virus / Plasmid: pPicZalpha / Production host: Pichia pastoris (fungus) / References: UniProt: Q2F842, UniProt: P52584*PLUS
#2: 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: 47694.164 Da / Num. of mol.: 1 / Fragment: VEGFR-2, UNP residues 132-548 / Mutation: Ig-domains 2-3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDR, FLK1, VEGFR2 / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf21
References: UniProt: P35968, receptor protein-tyrosine kinase

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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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M HEPES (pH 6.5), 0.8 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2010
RadiationMonochromator: LN2 cooled fixed exit SI8111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→67.8 Å / Num. obs: 11338 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.94 / Net I/σ(I): 11.3
Reflection shellResolution: 3.2→3.4 Å / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.2 / % possible all: 97.7

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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

Resolution: 3.205→67.789 Å / SU ML: 0.41 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 543 4.79 %random
Rwork0.2373 ---
obs0.2392 11338 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.998 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.4637 Å20 Å2-0 Å2
2---9.4637 Å2-0 Å2
3----20.7912 Å2
Refinement stepCycle: LAST / Resolution: 3.205→67.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 0 0 2093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052140
X-RAY DIFFRACTIONf_angle_d0.892906
X-RAY DIFFRACTIONf_dihedral_angle_d14.682756
X-RAY DIFFRACTIONf_chiral_restr0.052341
X-RAY DIFFRACTIONf_plane_restr0.003376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2047-3.52720.34711460.30422560X-RAY DIFFRACTION99
3.5272-4.03760.31111390.25272634X-RAY DIFFRACTION100
4.0376-5.08670.23171190.18022701X-RAY DIFFRACTION100
5.0867-67.80380.26771390.25252900X-RAY DIFFRACTION99
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)
11.2728-0.6214-0.11681.0734-0.56510.7454-0.1356-0.2713-0.0272-0.7473-0.73670.35460.5595-0.2426-0.34950.8384-0.53070.14640.26210.20990.266423.7843-18.530521.1181
20.6747-0.4118-0.15670.27340.23790.24670.0942-0.32760.36510.7369-0.2949-0.0427-0.0141-0.1131-0.00080.91060.0464-0.07530.63850.15050.875830.849811.682610.3504
30.77490.1956-0.11240.0949-0.00540.013-0.1340.21830.38970.7359-0.0265-0.94930.9291-0.2385-0.10681.38670.3822-0.1920.450.26221.188551.6902-25.95123.7088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain R and resseq 131:219
3X-RAY DIFFRACTION3chain R and resseq 220:329

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