[English] 日本語
Yorodumi
- PDB-2vpf: VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS RESO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vpf
TitleVASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS RESOLUTION
ComponentsVASCULAR ENDOTHELIAL GROWTH FACTOR
KeywordsGROWTH FACTOR / CYSTINE KNOT / ANGIOGENESIS / VASCULOGENESIS
Function / homology
Function and homology information


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 ...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 / negative regulation of adherens junction organization / post-embryonic camera-type eye development / 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 / 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 / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / 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 / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / artery morphogenesis / cardiac muscle cell development / sprouting angiogenesis / positive regulation of positive chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / vascular endothelial growth factor signaling pathway / 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 / positive regulation of focal adhesion assembly / 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 / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / epithelial cell differentiation / extracellular matrix / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / negative regulation of miRNA transcription / platelet alpha granule lumen / VEGFR2 mediated cell proliferation / secretory granule / kidney development / cytokine activity / positive regulation of epithelial cell proliferation
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 / Cystine Knot Cytokines, subunit B ...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: 1.93 Å
AuthorsMuller, Y.A. / De Vos, A.M.
Citation
Journal: Structure / Year: 1997
Title: The crystal structure of vascular endothelial growth factor (VEGF) refined to 1.93 A resolution: multiple copy flexibility and receptor binding.
Authors: Muller, Y.A. / Christinger, H.W. / Keyt, B.A. / de Vos, A.M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Vascular Endothelial Growth Factor: Crystal Structure and Functional Mapping of the Kinase Domain Receptor Binding Site
Authors: Muller, Y.A. / Li, B. / Christinger, H.W. / Wells, J.A. / Cunningham, B.C. / De Vos, A.M.
#2: Journal: Proteins / Year: 1996
Title: Crystallization of the Receptor Binding Domain of Vascular Endothelial Growth Factor
Authors: Christinger, H.W. / Muller, Y.A. / Berleau, L.T. / Keyt, B.A. / Cunningham, B.C. / Ferrara, N. / De Vos, A.M.
History
DepositionJul 29, 1997Processing site: BNL
Revision 1.0Jul 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VASCULAR ENDOTHELIAL GROWTH FACTOR
B: VASCULAR ENDOTHELIAL GROWTH FACTOR
C: VASCULAR ENDOTHELIAL GROWTH FACTOR
D: VASCULAR ENDOTHELIAL GROWTH FACTOR
E: VASCULAR ENDOTHELIAL GROWTH FACTOR
F: VASCULAR ENDOTHELIAL GROWTH FACTOR
G: VASCULAR ENDOTHELIAL GROWTH FACTOR
H: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)95,5898
Polymers95,5898
Non-polymers00
Water11,530640
1
C: VASCULAR ENDOTHELIAL GROWTH FACTOR
D: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)23,8972
Polymers23,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-24 kcal/mol
Surface area11200 Å2
MethodPISA
2
A: VASCULAR ENDOTHELIAL GROWTH FACTOR
B: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)23,8972
Polymers23,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-25 kcal/mol
Surface area11570 Å2
MethodPISA
3
E: VASCULAR ENDOTHELIAL GROWTH FACTOR
F: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)23,8972
Polymers23,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-26 kcal/mol
Surface area11670 Å2
MethodPISA
4
G: VASCULAR ENDOTHELIAL GROWTH FACTOR
H: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)23,8972
Polymers23,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-26 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.470, 68.470, 85.820
Angle α, β, γ (deg.)105.44, 93.71, 101.49
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.34321, -0.52364, -0.77974), (-0.53222, -0.57561, 0.62082), (-0.77391, 0.62807, -0.08114)-1.08611, 0.54147, -1.1872
2given(0.00287, -0.22, -0.9755), (0.4764, 0.85798, -0.1921), (0.87922, -0.46418, 0.10727)62.53261, -0.08027, 5.22423
3given(-0.91736, 0.01658, 0.3977), (0.27428, -0.69774, 0.66176), (0.28847, 0.71615, 0.63554)-29.25429, -26.73726, -49.50043
4given(0.36141, 0.27047, 0.89232), (0.2573, -0.94878, 0.18337), (0.8962, 0.16332, -0.41248)-41.65716, -19.30638, 5.22588
5given(-0.95462, 0.29008, -0.0675), (0.21043, 0.49658, -0.8421), (-0.21075, -0.81809, -0.53508)18.67854, 37.36586, 18.51475
6given(0.86923, -0.4668, -0.16292), (-0.46869, -0.88288, 0.02903), (-0.15739, 0.05112, -0.98621)-3.92029, 36.54798, 22.71535
7given(0.09535, 0.60375, 0.79145), (-0.32205, 0.77103, -0.54936), (-0.94191, -0.20251, 0.26795)-37.17354, -2.72744, 21.8472

-
Components

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


Mass: 11948.680 Da / Num. of mol.: 8 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P15692
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: HANGING DROP, CRYSTALLIZED FROM 14 % PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 mMTris-HCl1drop
30.4 M1dropNaCl
414 %PEG33501reservoir
510 %isopropanol1reservoir
60.2 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Mar 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 72050 / % possible obs: 94 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.5 % / Rsym value: 0.127 / % possible all: 80.8
Reflection
*PLUS
Num. measured all: 180803
Reflection shell
*PLUS
% possible obs: 81 % / Rmerge(I) obs: 0.127

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VPF

1vpf


Resolution: 1.93→16 Å / Cross valid method: THROUGHOUT
Details: AN EXPLICIT BULK SOLVENT MASK WAS CALCULATED WITH PROGRAM X-PLOR AND INTRODUCED INTO REFMAC USING PARTIAL STRUCTURE FACTORS (F-PART)
RfactorNum. reflection% reflectionSelection details
Rfree0.272 7074 10 %RESOLUTION SHELLS
Rwork0.209 ---
obs-68901 94 %-
Displacement parametersBiso mean: 47.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.56 Å20.76 Å21.22 Å2
2--3.09 Å21.64 Å2
3---5.47 Å2
Refine analyzeLuzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.93→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6142 0 0 640 6782
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.012.5
X-RAY DIFFRACTIONp_mcangle_it2.7784
X-RAY DIFFRACTIONp_scbond_it2.4682.5
X-RAY DIFFRACTIONp_scangle_it3.8924
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1130.15
X-RAY DIFFRACTIONp_singtor_nbd0.1790.3
X-RAY DIFFRACTIONp_multtor_nbd0.2430.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1890.3
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor18.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 68901 / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more