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- PDB-1qty: VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF TH... -

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Basic information

Entry
Database: PDB / ID: 1qty
TitleVASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR
Components
  • FMS-LIKE TYROSINE KINASE 1
  • VASCULAR ENDOTHELIAL GROWTH FACTOR
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / COMPLEX (GROWTH FACTOR-RECEPTOR) / FLT-1 / VEGF RECEPTOR / RECEPTOR TYROSINE KINASE / CYSTINE KNOT / GLYCOPROTEIN / IMMUNOGLOBULIN-LIKE DOMAIN / I-SET / HORMONE-GROWTH FACTOR RECEPTOR complex
Function / homology
Function and homology information


vascular endothelial growth factor receptor-1 signaling pathway / 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 / 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-1 signaling pathway / 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 / 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 / hyaloid vascular plexus regression / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / lymph vessel morphogenesis / primitive erythrocyte differentiation / 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 / bone trabecula formation / coronary vein morphogenesis / lung vasculature development / cardiac vascular smooth muscle cell development / lymphangiogenesis / Neurophilin interactions with VEGF and VEGFR / endothelial cell chemotaxis / positive regulation of trophoblast cell migration / vascular endothelial growth factor receptor-2 signaling pathway / positive regulation of epithelial tube formation / VEGF binds to VEGFR leading to receptor dimerization / motor neuron migration / regulation of nitric oxide mediated signal transduction / positive regulation of protein localization to early endosome / eye photoreceptor cell development / positive regulation of axon extension involved in axon guidance / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / embryonic morphogenesis / camera-type eye morphogenesis / positive regulation of branching involved in ureteric bud morphogenesis / neuropilin binding / coronary artery morphogenesis / induction of positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / commissural neuron axon guidance / dopaminergic neuron differentiation / tube formation / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of vascular permeability / positive regulation of blood vessel branching / platelet-derived growth factor receptor binding / surfactant homeostasis / endothelial cell proliferation / extracellular matrix binding / cell migration involved in sprouting angiogenesis / epithelial cell maturation / negative regulation of vascular endothelial cell proliferation / positive regulation of leukocyte migration / positive regulation of positive chemotaxis / cardiac muscle cell development / sprouting angiogenesis / blood vessel morphogenesis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of endothelial cell chemotaxis / vascular endothelial growth factor signaling pathway / artery morphogenesis / negative regulation of epithelial to mesenchymal transition / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / negative regulation of fat cell differentiation / positive chemotaxis / growth factor binding / positive regulation of sprouting angiogenesis / chemoattractant activity / mesoderm development / monocyte chemotaxis / outflow tract morphogenesis / positive regulation of protein autophosphorylation / monocyte differentiation / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of receptor internalization / mammary gland alveolus development / neuroblast proliferation / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / positive regulation of blood vessel endothelial cell migration / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / heart morphogenesis
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 ...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 / VEGFR1-3, N-terminal 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 / 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. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / Immunoglobulins / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT IN COMBINATION WITH MULTI-CRYSTAL AVERAGING / Resolution: 2.7 Å
AuthorsWiesmann, C. / de Vos, A.M.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Solution structure of the VEGF-binding domain of Flt-1: comparison of its free and bound states.
Authors: Starovasnik, M.A. / Christinger, H.W. / Wiesmann, C. / Champe, M.A. / de Vos, A.M. / Skelton, N.J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystal Structure at 1.7 A Resolution of Vegf in Complex with Domain 2 of the Flt-1 Receptor
Authors: Wiesmann, C. / Fuh, G. / Christinger, H.W. / Eigenbrot, C. / Wells, J.A. / de Vos, A.M.
History
DepositionJun 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: VASCULAR ENDOTHELIAL GROWTH FACTOR
W: VASCULAR ENDOTHELIAL GROWTH FACTOR
R: VASCULAR ENDOTHELIAL GROWTH FACTOR
S: VASCULAR ENDOTHELIAL GROWTH FACTOR
X: FMS-LIKE TYROSINE KINASE 1
Y: FMS-LIKE TYROSINE KINASE 1
T: FMS-LIKE TYROSINE KINASE 1
U: FMS-LIKE TYROSINE KINASE 1


Theoretical massNumber of molelcules
Total (without water)93,9488
Polymers93,9488
Non-polymers00
Water00
1
V: VASCULAR ENDOTHELIAL GROWTH FACTOR
W: VASCULAR ENDOTHELIAL GROWTH FACTOR
X: FMS-LIKE TYROSINE KINASE 1
Y: FMS-LIKE TYROSINE KINASE 1


Theoretical massNumber of molelcules
Total (without water)46,9744
Polymers46,9744
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-51 kcal/mol
Surface area19250 Å2
MethodPISA
2
R: VASCULAR ENDOTHELIAL GROWTH FACTOR
S: VASCULAR ENDOTHELIAL GROWTH FACTOR
T: FMS-LIKE TYROSINE KINASE 1
U: FMS-LIKE TYROSINE KINASE 1


Theoretical massNumber of molelcules
Total (without water)46,9744
Polymers46,9744
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-51 kcal/mol
Surface area19330 Å2
MethodPISA
3
R: VASCULAR ENDOTHELIAL GROWTH FACTOR
S: VASCULAR ENDOTHELIAL GROWTH FACTOR
T: FMS-LIKE TYROSINE KINASE 1
U: FMS-LIKE TYROSINE KINASE 1

V: VASCULAR ENDOTHELIAL GROWTH FACTOR
W: VASCULAR ENDOTHELIAL GROWTH FACTOR
X: FMS-LIKE TYROSINE KINASE 1
Y: FMS-LIKE TYROSINE KINASE 1


Theoretical massNumber of molelcules
Total (without water)93,9488
Polymers93,9488
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area15870 Å2
ΔGint-121 kcal/mol
Surface area34850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.31, 67.01, 120.84
Angle α, β, γ (deg.)90, 118.15, 90
Int Tables number5
Space group name H-MC121
DetailsCHAINS V, W, X, and Y FORM A BIOLOGICALLY ACTIVE COMPLEX. CHAINS R, S, T, and U FORM A BIOLOGICALLY ACTIVE COMPLEX.

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Components

#1: Protein
VASCULAR ENDOTHELIAL GROWTH FACTOR


Mass: 11948.680 Da / Num. of mol.: 4 / Fragment: RECEPTOR BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P15692
#2: Protein
FMS-LIKE TYROSINE KINASE 1 / FLT-1


Mass: 11538.298 Da / Num. of mol.: 4 / Fragment: DOMAIN 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P17948
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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Wiesmann, C., (1997) Cell, 91, 695.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
220 mMTris-HCl1drop
330 %PEG40001reservoir
40.2 Mammonium sulfate1reservoir
50.02 %1reservoirNaN3
60.15 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 24, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 24216 / Num. obs: 24098 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.049 / Net I/σ(I): 13.3
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 3 % / Num. unique all: 1544 / Rsym value: 0.311 / % possible all: 98

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DMmodel building
X-PLOR3.851refinement
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT IN COMBINATION WITH MULTI-CRYSTAL AVERAGING
Starting model: 1VPF

1vpf


Resolution: 2.7→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R / σ(F): 0.2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 1127 4.5 %RANDOM
Rwork0.2327 ---
obs0.2327 23438 92.6 %-
all-23438 --
Displacement parametersBiso mean: 63.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å2-1.3 Å2
2---7.6 Å20 Å2
3---8.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6121 0 0 0 6121
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_mcbond_it1.91.5
X-RAY DIFFRACTIONx_mcangle_it2.52
X-RAY DIFFRACTIONx_scbond_it3.42
X-RAY DIFFRACTIONx_scangle_it3.52.5
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4 136 4.5 %
Rwork0.383 2436 -
obs--85 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_mcbond_it1.91.5
X-RAY DIFFRACTIONx_scbond_it3.42
X-RAY DIFFRACTIONx_mcangle_it2.52
X-RAY DIFFRACTIONx_scangle_it3.52.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.4 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.383

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