[English] 日本語
Yorodumi
- PDB-3v6b: VEGFR-2/VEGF-E complex structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v6b
TitleVEGFR-2/VEGF-E complex structure
Components
  • VEGF-E
  • Vascular endothelial growth factor receptor 2
KeywordsHORMONE/SIGNALING PROTEIN / Ig-homology domain / VEGFR-2 / growth factor receptor / VEGF ligand / ANGIOGENESIS / MEMBRANE / VEGF-E / Orf virus / HORMONE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


positive regulation of nitric oxide-cGMP mediated signal transduction / blood vessel endothelial cell differentiation / vascular endothelial growth factor receptor binding / regulation of bone development / cellular response to hydrogen sulfide / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / Neuropilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization ...positive regulation of nitric oxide-cGMP mediated signal transduction / blood vessel endothelial cell differentiation / vascular endothelial growth factor receptor binding / regulation of bone development / cellular response to hydrogen sulfide / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / Neuropilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / endocardium development / endothelium development / regulation of hematopoietic progenitor cell differentiation / vascular endothelial growth factor receptor activity / mesenchymal cell proliferation / post-embryonic camera-type eye morphogenesis / endothelial cell differentiation / lymph vessel development / positive regulation of vasculogenesis / vascular wound healing / induction of positive chemotaxis / positive regulation of BMP signaling pathway / surfactant homeostasis / epithelial cell maturation / anchoring junction / positive regulation of positive chemotaxis / positive regulation of endothelial cell chemotaxis / embryonic hemopoiesis / positive regulation of mesenchymal cell proliferation / positive regulation of cell migration involved in sprouting angiogenesis / vascular endothelial growth factor signaling pathway / lung alveolus development / positive regulation of mitochondrial fission / branching involved in blood vessel morphogenesis / positive regulation of stem cell proliferation / growth factor binding / sorting endosome / chemoattractant activity / positive regulation of mitochondrial depolarization / semaphorin-plexin signaling pathway / positive regulation of cell division / regulation of MAPK cascade / positive regulation of macroautophagy / 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 / cell fate commitment / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / vasculogenesis / ovarian follicle development / coreceptor activity / calcium ion homeostasis / peptidyl-tyrosine phosphorylation / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / epithelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / stem cell proliferation / VEGFR2 mediated cell proliferation / growth factor activity / receptor protein-tyrosine kinase / Hsp90 protein binding / positive regulation of protein phosphorylation / VEGFA-VEGFR2 Pathway / integrin binding / positive regulation of angiogenesis / cell junction / protein autophosphorylation / regulation of cell shape / cell migration / protein tyrosine kinase activity / angiogenesis / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / negative regulation of neuron apoptotic process / response to hypoxia / early endosome / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / signaling receptor complex / endosome / positive regulation of cell migration / cadherin binding / membrane raft / external side of plasma membrane / negative regulation of gene expression / positive regulation of cell population proliferation / endoplasmic reticulum / Golgi apparatus / : / extracellular region / ATP binding / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Vascular endothelial growth factor receptor 2 (VEGFR2) / 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 ...Vascular endothelial growth factor receptor 2 (VEGFR2) / 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 / Immunoglobulin domain / Cystine-knot cytokine / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ribbon / 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 receptor 2 / Vascular endothelial growth factor homolog / VEGF-E
Similarity search - Component
Biological speciesOrf virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.205 Å
AuthorsBrozzo, M.S. / Leppanen, V.-M. / Winkler, F.K. / Kisko, K. / Ballmer-Hofer, K.
CitationJournal: Blood / Year: 2012
Title: Thermodynamic and structural description of allosterically regulated VEGFR-2 dimerization.
Authors: Brozzo, M.S. / Bjelic, S. / Kisko, K. / Schleier, T. / Leppanen, V.M. / Alitalo, K. / Winkler, F.K. / Ballmer-Hofer, K.
History
DepositionDec 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 3, 2024Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VEGF-E
R: Vascular endothelial growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)63,1992
Polymers63,1992
Non-polymers00
Water00
1
A: VEGF-E
R: Vascular endothelial growth factor receptor 2

A: VEGF-E
R: Vascular endothelial growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)126,3974
Polymers126,3974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area6940 Å2
ΔGint-46 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.879, 79.879, 340.044
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein VEGF-E


Mass: 15504.567 Da / Num. of mol.: 1 / Fragment: VEGF-E, UNP residues 21-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orf virus / Plasmid: pPicZalpha / Production host: Pichia pastoris (fungus) / References: UniProt: Q2F842, UniProt: P52584*PLUS
#2: Protein Vascular endothelial growth factor receptor 2 / VEGFR-2 / Fetal liver kinase 1 / FLK-1 / Kinase insert domain receptor / KDR / Protein-tyrosine ...VEGFR-2 / Fetal liver kinase 1 / FLK-1 / Kinase insert domain receptor / KDR / Protein-tyrosine kinase receptor flk-1


Mass: 47694.164 Da / Num. of mol.: 1 / Fragment: VEGFR-2, UNP residues 132-548 / Mutation: Ig-domains 2-3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDR, FLK1, VEGFR2 / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf21
References: UniProt: P35968, receptor protein-tyrosine kinase
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M HEPES (pH 6.5), 0.8 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2010
RadiationMonochromator: LN2 cooled fixed exit SI8111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→67.8 Å / Num. obs: 11338 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.94 / Net I/σ(I): 11.3
Reflection shellResolution: 3.2→3.4 Å / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.2 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VEGF-E

Resolution: 3.205→67.789 Å / SU ML: 0.41 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 543 4.79 %random
Rwork0.2373 ---
obs0.2392 11338 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.998 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.4637 Å20 Å2-0 Å2
2---9.4637 Å2-0 Å2
3----20.7912 Å2
Refinement stepCycle: LAST / Resolution: 3.205→67.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 0 0 2093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052140
X-RAY DIFFRACTIONf_angle_d0.892906
X-RAY DIFFRACTIONf_dihedral_angle_d14.682756
X-RAY DIFFRACTIONf_chiral_restr0.052341
X-RAY DIFFRACTIONf_plane_restr0.003376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2047-3.52720.34711460.30422560X-RAY DIFFRACTION99
3.5272-4.03760.31111390.25272634X-RAY DIFFRACTION100
4.0376-5.08670.23171190.18022701X-RAY DIFFRACTION100
5.0867-67.80380.26771390.25252900X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2728-0.6214-0.11681.0734-0.56510.7454-0.1356-0.2713-0.0272-0.7473-0.73670.35460.5595-0.2426-0.34950.8384-0.53070.14640.26210.20990.266423.7843-18.530521.1181
20.6747-0.4118-0.15670.27340.23790.24670.0942-0.32760.36510.7369-0.2949-0.0427-0.0141-0.1131-0.00080.91060.0464-0.07530.63850.15050.875830.849811.682610.3504
30.77490.1956-0.11240.0949-0.00540.013-0.1340.21830.38970.7359-0.0265-0.94930.9291-0.2385-0.10681.38670.3822-0.1920.450.26221.188551.6902-25.95123.7088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain R and resseq 131:219
3X-RAY DIFFRACTION3chain R and resseq 220:329

+
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