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- PDB-5t89: Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6 -

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Basic information

Entry
Database: PDB / ID: 5t89
TitleCrystal structure of VEGF-A in complex with VEGFR-1 domains D1-6
Components
  • Vascular endothelial growth factor A
  • Vascular endothelial growth factor receptor 1VEGF receptor
KeywordsTRANSFERASE / receptor tyrosine kinase / growth factor / immunoglobulin domain
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 / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier ...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 / 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 / positive regulation of peptidyl-tyrosine autophosphorylation / post-embryonic camera-type eye development / negative regulation of adherens junction organization / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / VEGF-activated neuropilin signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / motor neuron migration / Neurophilin interactions with VEGF and VEGFR / positive regulation of trophoblast cell migration / endothelial cell chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / eye photoreceptor cell development / 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 cell migration by vascular endothelial growth factor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of protein localization to early endosome / vascular wound healing / vascular endothelial growth factor receptor activity / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / embryonic morphogenesis / camera-type eye morphogenesis / positive regulation of epithelial tube formation / negative regulation of cell-cell adhesion mediated by cadherin / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / vascular endothelial growth factor receptor 2 binding / commissural neuron axon guidance / positive regulation of vascular permeability / dopaminergic neuron differentiation / surfactant homeostasis / positive regulation of endothelial cell chemotaxis / platelet-derived growth factor receptor binding / extracellular matrix binding / retinal ganglion cell axon guidance / cell migration involved in sprouting angiogenesis / artery morphogenesis / cardiac muscle cell development / sprouting angiogenesis / negative regulation of vascular endothelial cell proliferation / positive regulation of positive chemotaxis / blood vessel morphogenesis / vascular endothelial growth factor signaling pathway / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of leukocyte migration / positive regulation of p38MAPK cascade / positive regulation of DNA biosynthetic process / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / activation of protein kinase activity / chemoattractant activity / growth factor binding / positive regulation of focal adhesion assembly / monocyte chemotaxis / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / positive regulation of cell division / macrophage differentiation / fibronectin binding / positive regulation of cell adhesion / positive regulation of blood vessel endothelial cell migration / mammary gland alveolus development / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / positive regulation of phospholipase C activity / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / epithelial cell differentiation / lactation
Similarity search - Function
Vascular endothelial growth factor receptor 1 (VEGFR1) / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / 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 ...Vascular endothelial growth factor receptor 1 (VEGFR1) / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / 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 / Cystine-knot cytokine / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / 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 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form / Vascular endothelial growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4 Å
AuthorsMarkovic-Mueller, S. / Stuttfeld, E. / Asthana, M. / Weinert, T. / Bliven, S. / Goldie, K.N. / Kisko, K. / Capitani, G. / Ballmer-Hofer, K.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-130463 Switzerland
OncosuisseOC2 01200-08-2007 Switzerland
CitationJournal: Structure / Year: 2017
Title: Structure of the Full-length VEGFR-1 Extracellular Domain in Complex with VEGF-A.
Authors: Markovic-Mueller, S. / Stuttfeld, E. / Asthana, M. / Weinert, T. / Bliven, S. / Goldie, K.N. / Kisko, K. / Capitani, G. / Ballmer-Hofer, K.
History
DepositionSep 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Advisory / Author supporting evidence / Data collection
Category: diffrn_radiation_wavelength / pdbx_audit_support / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A
X: Vascular endothelial growth factor receptor 1
Y: Vascular endothelial growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,19125
Polymers177,1394
Non-polymers5,05221
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15870 Å2
ΔGint-8 kcal/mol
Surface area79300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.710, 123.090, 167.370
Angle α, β, γ (deg.)90.000, 109.560, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vascular endothelial growth factor A / / VEGF-A / Vascular permeability factor / VPF


Mass: 15195.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGFA, VEGF / Plasmid: pPICZalpha / Production host: Komagataella pastoris (fungus) / References: UniProt: P15692
#2: Protein Vascular endothelial growth factor receptor 1 / VEGF receptor / VEGFR-1 / Fms-like tyrosine kinase 1 / FLT-1 / Tyrosine-protein kinase FRT / Tyrosine-protein ...VEGFR-1 / Fms-like tyrosine kinase 1 / FLT-1 / Tyrosine-protein kinase FRT / Tyrosine-protein kinase receptor FLT / FLT / Vascular permeability factor receptor


Mass: 73374.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLT1, FLT, FRT, VEGFR1 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21
References: UniProt: P17948, receptor protein-tyrosine kinase
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 4.9 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 10-14% PEG3000 200 mM calcium chloride 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 7, 2014
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 26988 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 138.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.53
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
4-4.12.0021.180.549199.3
4.1-4.221.5231.520.684199.3
4.22-4.341.0042.280.848199.5
4.34-4.470.7932.750.877199.4
4.47-4.620.6143.350.925199.3
4.62-4.780.4944.010.925199.5
4.78-4.960.444.710.939199.2
4.96-5.160.3825.250.9571100
5.16-5.390.3656.150.966199.6
5.39-5.660.3166.770.971199.6
5.66-5.960.2957.280.973199.5
5.96-6.320.3047.070.97199.8
6.32-6.760.229.110.987199.5
6.76-7.30.13813.490.994199.3
7.3-80.09818.160.996199.3
8-8.940.06125.030.998199.9
8.94-10.330.04234.530.998199.8
10.33-12.650.03642.610.9991100
12.65-17.890.03546.290.999199.1
17.890.02652.150.999194

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Processing

Software
NameVersionClassification
PHENIXdev_2420refinement
XSCALEVersion January 10, 2014data scaling
PDB_EXTRACT3.2data extraction
XDSVersion January 10, 2014data reduction
PHASER2.5.6phasing
RefinementMethod to determine structure: SAD / Resolution: 4→19.988 Å / SU ML: 0.75 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 40.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3153 802 3 %
Rwork0.285 25938 -
obs0.286 26740 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 481.09 Å2 / Biso mean: 223.7936 Å2 / Biso min: 93.11 Å2
Refinement stepCycle: final / Resolution: 4→19.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11035 0 322 0 11357
Biso mean--277.36 --
Num. residues----1356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411616
X-RAY DIFFRACTIONf_angle_d0.7115760
X-RAY DIFFRACTIONf_chiral_restr0.051862
X-RAY DIFFRACTIONf_plane_restr0.0051960
X-RAY DIFFRACTIONf_dihedral_angle_d11.0027075
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0001-4.24840.45521320.38424264439699
4.2484-4.57280.35361320.32634299443199
4.5728-5.02640.32261330.2934285441899
5.0264-5.73860.29241350.28943644499100
5.7386-7.1740.34651330.322843264459100
7.174-19.98810.26651370.228644004537100

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