[English] 日本語
Yorodumi
- PDB-2c7w: Crystal Structure of human vascular endothelial growth factor-B: ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c7w
TitleCrystal Structure of human vascular endothelial growth factor-B: Identification of amino acids important for angiogeninc activity
ComponentsVASCULAR ENDOTHELIAL GROWTH FACTOR B PRECURSOR
KeywordsGROWTH FACTOR / VASCULAR ENDOTHELIAL GROWTH FACTOR-B / ANGIOGENESIS / CYSTEINE-KNOT MOTIF / TYROSINE KINASE / ISCHEMIA / MITOGEN / GLYCOPROTEIN / HEPARIN-BINDING
Function / homology
Function and homology information


positive regulation of vascular wound healing / vascular endothelial growth factor receptor 1 binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / VEGF binds to VEGFR leading to receptor dimerization / induction of positive chemotaxis / vascular endothelial growth factor receptor 2 binding / protein O-linked glycosylation / coronary vasculature development / positive regulation of vascular endothelial growth factor receptor signaling pathway ...positive regulation of vascular wound healing / vascular endothelial growth factor receptor 1 binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / VEGF binds to VEGFR leading to receptor dimerization / induction of positive chemotaxis / vascular endothelial growth factor receptor 2 binding / protein O-linked glycosylation / coronary vasculature development / positive regulation of vascular endothelial growth factor receptor signaling pathway / sprouting angiogenesis / vascular endothelial growth factor signaling pathway / chemoattractant activity / positive regulation of cell division / vascular endothelial growth factor receptor signaling pathway / cardiac muscle contraction / positive regulation of endothelial cell proliferation / platelet alpha granule lumen / growth factor activity / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / Platelet degranulation / heparin binding / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / positive regulation of protein phosphorylation / negative regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular region / membrane / identical protein binding
Similarity search - Function
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 B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsIyer, S. / Scotney, P.D. / Nash, A.D. / Acharya, K.R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Human Vascular Endothelial Growth Factor-B: Identification of Amino Acids Important for Receptor Binding
Authors: Iyer, S. / Scotney, P.D. / Nash, A.D. / Acharya, K.R.
History
DepositionNov 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VASCULAR ENDOTHELIAL GROWTH FACTOR B PRECURSOR
B: VASCULAR ENDOTHELIAL GROWTH FACTOR B PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4323
Polymers22,3142
Non-polymers1181
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)120.806, 120.806, 39.826
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

-
Components

#1: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR B PRECURSOR / VASCULAR ENDOTHELIAL GROWTH FACTOR-B / VEGF-B / VEGF RELATED FACTOR


Mass: 11157.050 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49765
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Compound detailsWORK AS A GROWTH FACTOR FOR ENDOTHELIAL CELLS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.1 %
Crystal growpH: 6.8
Details: 0.1M HEPES (PH 6.8), 0.5M AMMONIUM SULPHATE 50%, MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 18, 2003 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.48→40 Å / Num. obs: 12054 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 43.1 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.9
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VPF

2vpf


Resolution: 2.48→40 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 441769.31 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31 712 5.9 %RANDOM
Rwork0.286 ---
obs0.286 10937 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.1563 Å2 / ksol: 0.379841 e/Å3
Displacement parametersBiso mean: 40.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.48→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 8 74 1474
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.48→2.57 Å / Rfactor Rwork: 0.312 / Total num. of bins used: 6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MPD.PARAMMPD.TOP

+
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