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- PDB-1vpp: COMPLEX BETWEEN VEGF AND A RECEPTOR BLOCKING PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1vpp
TitleCOMPLEX BETWEEN VEGF AND A RECEPTOR BLOCKING PEPTIDE
Components
  • PROTEIN (PEPTIDE V108)
  • PROTEIN (VASCULAR ENDOTHELIAL GROWTH FACTOR)
KeywordsGROWTH FACTOR/GROWTH FACTOR INHIBITOR / CYSTINE KNOT / ANGIOGENESIS / VASCULOGENESIS / RECEPTOR BLOCKING PEPTIDE / GROWTH FACTOR-GROWTH FACTOR INHIBITOR COMPLEX
Function / homology
Function and homology information


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 / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor 1 binding ...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 / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor 1 binding / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor binding / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / negative regulation of blood-brain barrier permeability / VEGF-activated neuropilin signaling pathway / bone trabecula formation / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / lung vasculature development / cardiac vascular smooth muscle cell development / lymphangiogenesis / eye photoreceptor cell development / endothelial cell chemotaxis / positive regulation of trophoblast cell migration / positive regulation of epithelial tube formation / vascular endothelial growth factor receptor-2 signaling pathway / motor neuron migration / VEGF binds to VEGFR leading to receptor dimerization / regulation of nitric oxide mediated signal transduction / positive regulation of axon extension involved in axon guidance / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / positive regulation of protein localization to early endosome / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / camera-type eye morphogenesis / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular permeability / dopaminergic neuron differentiation / tube formation / commissural neuron axon guidance / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / cardiac muscle cell development / epithelial cell maturation / sprouting angiogenesis / positive regulation of positive chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / endothelial cell proliferation / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of endothelial cell chemotaxis / artery morphogenesis / positive regulation of p38MAPK cascade / negative regulation of epithelial to mesenchymal transition / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive chemotaxis / positive regulation of neuroblast proliferation / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of fat cell differentiation / positive regulation of sprouting angiogenesis / chemoattractant activity / positive regulation of focal adhesion assembly / outflow tract morphogenesis / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / neuroblast proliferation / mammary gland alveolus development / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / homeostasis of number of cells within a tissue / epithelial cell differentiation / positive regulation of endothelial cell proliferation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell migration
Similarity search - Function
Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding 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, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWiesmann, C. / Christinger, H.W. / Cochran, A.G. / Cunningham, B.C. / Fairbrother, W.J. / Keenan, C.J. / Meng, G. / de Vos, A.M.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of the complex between VEGF and a receptor-blocking peptide.
Authors: Wiesmann, C. / Christinger, H.W. / Cochran, A.G. / Cunningham, B.C. / Fairbrother, W.J. / Keenan, C.J. / Meng, G. / de Vos, A.M.
History
DepositionOct 9, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 1.4Nov 20, 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: PROTEIN (VASCULAR ENDOTHELIAL GROWTH FACTOR)
W: PROTEIN (VASCULAR ENDOTHELIAL GROWTH FACTOR)
X: PROTEIN (PEPTIDE V108)
Y: PROTEIN (PEPTIDE V108)


Theoretical massNumber of molelcules
Total (without water)28,4144
Polymers28,4144
Non-polymers00
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-36 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.703, 74.661, 79.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.48459, 0.84119, -0.23993), (0.84395, -0.52173, -0.12463), (-0.23002, -0.14209, -0.96275)
Vector: -5.456, 18.511, 29.694)

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Components

#1: Protein PROTEIN (VASCULAR ENDOTHELIAL GROWTH FACTOR) / VEGF / VASCULAR PERMEABILITY FACTOR / VPF


Mass: 11948.680 Da / Num. of mol.: 2 / 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/peptide PROTEIN (PEPTIDE V108)


Mass: 2258.491 Da / Num. of mol.: 2 / Fragment: RECEPTOR BLOCKING PEPTIDE / Source method: obtained synthetically / Details: THIS SEQUENCE IS CHEMICALLY SYNTHESIZED
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlpeptide1drop
230 %PEG40001reservoir
30.2 Mammonium sulfate1reservoir
40.1 Msodium acetate1reservoirpH5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→99 Å / Num. obs: 23253 / % possible obs: 99.6 % / Redundancy: 5.1 % / Rsym value: 0.06 / Net I/σ(I): 14.4
Reflection
*PLUS
Rmerge(I) obs: 0.045

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLT

1flt


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1345 6.3 %RANDOM
Rwork0.19 ---
obs0.19 16942 97.5 %-
Displacement parametersBiso mean: 27.1 Å2 /
Baniso -2Baniso -3
1-0 Å20 Å2
2--0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 0 383 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.47
X-RAY DIFFRACTIONp_mcangle_it3.3
X-RAY DIFFRACTIONp_scbond_it5.3
X-RAY DIFFRACTIONp_scangle_it6.7
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Num. reflection obs: 21270 / σ(F): 0 / % reflection Rfree: 6.3 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.040.03
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_mcbond_it2.47
X-RAY DIFFRACTIONp_scbond_it5.3
X-RAY DIFFRACTIONp_mcangle_it3.3
X-RAY DIFFRACTIONp_scangle_it6.7

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