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- PDB-1flt: VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1flt
TitleVEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR
Components
  • FMS-LIKE TYROSINE KINASE 1
  • VASCULAR ENDOTHELIAL GROWTH FACTOR
KeywordsCOMPLEX (GROWTH FACTOR/TRANSFERASE) / COMPLEX (GROWTH FACTOR-TRANSFERASE) / FLT-1 RECEPTOR / CYSTINE KNOT / GLYCOPROTEIN / IMMUNOGLOBULIN-LIKE DOMAIN TRANSFERASE / COMPLEX (GROWTH FACTOR-TRANSFERASE) complex
Function / homology
Function and homology information


vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / Signaling by VEGF / basophil chemotaxis / lymph vessel morphogenesis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / : / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor 1 binding ...vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / Signaling by VEGF / basophil chemotaxis / lymph vessel morphogenesis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / : / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor 1 binding / negative regulation of adherens junction organization / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of mast cell chemotaxis / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / 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 / hyaloid vascular plexus regression / motor neuron migration / eye photoreceptor cell development / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / mammary gland alveolus development / Neuropilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor-2 signaling pathway / vascular endothelial growth factor receptor activity / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of axon extension involved in axon guidance / camera-type eye morphogenesis / endothelial cell chemotaxis / positive regulation of protein localization to early endosome / positive regulation of trophoblast cell migration / surfactant homeostasis / retinal ganglion cell axon guidance / induction of positive chemotaxis / vascular wound healing / positive regulation of protein autophosphorylation / dopaminergic neuron differentiation / embryonic morphogenesis / positive regulation of epithelial tube formation / 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 / blood vessel morphogenesis / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular permeability / commissural neuron axon guidance / artery morphogenesis / cardiac muscle cell development / branching involved in blood vessel morphogenesis / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of blood vessel branching / sprouting angiogenesis / platelet-derived growth factor receptor binding / extracellular matrix binding / positive regulation of positive chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of neuroblast proliferation / negative regulation of vascular endothelial cell 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 / growth factor binding / positive chemotaxis / positive regulation of sprouting angiogenesis / mesoderm development / ovarian follicle development / positive regulation of MAP kinase activity / chemoattractant activity / cell maturation / outflow tract morphogenesis / lung development / vasculogenesis / macrophage differentiation / fibronectin binding / monocyte differentiation / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / heart morphogenesis / monocyte chemotaxis / positive regulation of receptor internalization / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / lactation / kidney development / positive regulation of endothelial cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / transmembrane receptor protein tyrosine kinase activity
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 / Vascular endothelial growth factor A, long form-like domain / VEGFR-2, transmembrane domain / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR-1-like, immunoglobulin-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 / Vascular endothelial growth factor A, long form-like domain / 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. / 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 / Ribbon / Immunoglobulin V-set domain / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT/NCS AVERAGING / Resolution: 1.7 Å
AuthorsWiesmann, C. / De Vos, A.M.
CitationJournal: 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
DepositionNov 20, 1997Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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)44,8364
Polymers44,8364
Non-polymers00
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-50 kcal/mol
Surface area20420 Å2
MethodPISA
2
V: VASCULAR ENDOTHELIAL GROWTH FACTOR
W: VASCULAR ENDOTHELIAL GROWTH FACTOR
X: FMS-LIKE TYROSINE KINASE 1
Y: 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)89,6728
Polymers89,6728
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16050 Å2
ΔGint-119 kcal/mol
Surface area37070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 71.130, 77.860
Angle α, β, γ (deg.)90.00, 105.28, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.74121, -0.28886, 0.60594), (-0.33155, -0.62734, -0.70464), (0.58367, -0.72319, 0.36922)-12.38126, 10.55189, 10.82224
2given(-0.82633, -0.18021, 0.53357), (-0.3462, -0.58473, -0.73365), (0.4442, -0.79096, 0.42079)-9.95226, 11.37281, 12.68678

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Components

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


Mass: 11511.249 Da / Num. of mol.: 2 / 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: Protein FMS-LIKE TYROSINE KINASE 1 / FLT-1 / VGR1


Mass: 10906.662 Da / Num. of mol.: 2
Fragment: SECOND EXTRACELLULAR IGG LIKE DOMAIN, RESIDUES 129 - 229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P17948, receptor protein-tyrosine kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
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: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Feb 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 47047 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.052 / Net I/σ(I): 8.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.27 / % possible all: 95.8
Reflection
*PLUS
Num. measured all: 332877 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 95.8 % / Num. unique obs: 4520 / Rmerge(I) obs: 0.277

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT/NCS AVERAGING
Starting model: 1VPF

1vpf


Resolution: 1.7→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2275 4.8 %RANDOM
Rwork0.198 ---
obs0.198 45678 96.8 %-
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.905 Å20 Å2-2.748 Å2
2---4.0386 Å20 Å2
3---2.1336 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 0 476 3566
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_deg1.76
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.99
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.42.5
X-RAY DIFFRACTIONx_mcangle_it4.95
X-RAY DIFFRACTIONx_scbond_it3.93.5
X-RAY DIFFRACTIONx_scangle_it6.36
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.35 257 4.4 %
Rwork0.32 5104 -
obs--91.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.99
LS refinement shell
*PLUS
Rfactor obs: 0.32

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