[English] 日本語
Yorodumi
- PDB-1qty: VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF TH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qty
TitleVASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR
Components
  • FMS-LIKE TYROSINE KINASE 1
  • VASCULAR ENDOTHELIAL GROWTH FACTOR
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / COMPLEX (GROWTH FACTOR-RECEPTOR) / FLT-1 / VEGF RECEPTOR / RECEPTOR TYROSINE KINASE / CYSTINE KNOT / GLYCOPROTEIN / IMMUNOGLOBULIN-LIKE DOMAIN / I-SET / HORMONE-GROWTH FACTOR RECEPTOR complex
Function / homology
Function and homology information


vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / 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-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / 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 / Neurophilin interactions with VEGF and VEGFR / 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 / vascular endothelial growth factor receptor activity / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / embryonic morphogenesis / 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 / negative regulation of vascular endothelial cell proliferation / positive regulation of positive chemotaxis / blood vessel morphogenesis / 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 / growth factor binding / positive regulation of focal adhesion assembly / monocyte chemotaxis / 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 / positive regulation of phospholipase C activity / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / epithelial cell differentiation / extracellular matrix
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 / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF 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 / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-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 / 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 / Immunoglobulin V-set domain / 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 / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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 / MOLECULAR REPLACEMENT IN COMBINATION WITH MULTI-CRYSTAL AVERAGING / Resolution: 2.7 Å
AuthorsWiesmann, C. / de Vos, A.M.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Solution structure of the VEGF-binding domain of Flt-1: comparison of its free and bound states.
Authors: Starovasnik, M.A. / Christinger, H.W. / Wiesmann, C. / Champe, M.A. / de Vos, A.M. / Skelton, N.J.
#1: Journal: 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
DepositionJun 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
V: VASCULAR ENDOTHELIAL GROWTH FACTOR
W: VASCULAR ENDOTHELIAL GROWTH FACTOR
R: VASCULAR ENDOTHELIAL GROWTH FACTOR
S: VASCULAR ENDOTHELIAL GROWTH FACTOR
X: FMS-LIKE TYROSINE KINASE 1
Y: FMS-LIKE TYROSINE KINASE 1
T: FMS-LIKE TYROSINE KINASE 1
U: FMS-LIKE TYROSINE KINASE 1


Theoretical massNumber of molelcules
Total (without water)93,9488
Polymers93,9488
Non-polymers00
Water0
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)46,9744
Polymers46,9744
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-51 kcal/mol
Surface area19250 Å2
MethodPISA
2
R: VASCULAR ENDOTHELIAL GROWTH FACTOR
S: VASCULAR ENDOTHELIAL GROWTH FACTOR
T: FMS-LIKE TYROSINE KINASE 1
U: FMS-LIKE TYROSINE KINASE 1


Theoretical massNumber of molelcules
Total (without water)46,9744
Polymers46,9744
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-51 kcal/mol
Surface area19330 Å2
MethodPISA
3
R: VASCULAR ENDOTHELIAL GROWTH FACTOR
S: VASCULAR ENDOTHELIAL GROWTH FACTOR
T: FMS-LIKE TYROSINE KINASE 1
U: 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)93,9488
Polymers93,9488
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area15870 Å2
ΔGint-121 kcal/mol
Surface area34850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.31, 67.01, 120.84
Angle α, β, γ (deg.)90, 118.15, 90
Int Tables number5
Space group name H-MC121
DetailsCHAINS V, W, X, and Y FORM A BIOLOGICALLY ACTIVE COMPLEX. CHAINS R, S, T, and U FORM A BIOLOGICALLY ACTIVE COMPLEX.

-
Components

#1: Protein
VASCULAR ENDOTHELIAL GROWTH FACTOR /


Mass: 11948.680 Da / Num. of mol.: 4 / 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
FMS-LIKE TYROSINE KINASE 1 / FLT-1


Mass: 11538.298 Da / Num. of mol.: 4 / Fragment: DOMAIN 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P17948

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Wiesmann, C., (1997) Cell, 91, 695.
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 24, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 24216 / Num. obs: 24098 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.049 / Net I/σ(I): 13.3
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 3 % / Num. unique all: 1544 / Rsym value: 0.311 / % possible all: 98

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DMmodel building
X-PLOR3.851refinement
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT IN COMBINATION WITH MULTI-CRYSTAL AVERAGING
Starting model: 1VPF

1vpf


Resolution: 2.7→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R / σ(F): 0.2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 1127 4.5 %RANDOM
Rwork0.2327 ---
obs0.2327 23438 92.6 %-
all-23438 --
Displacement parametersBiso mean: 63.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å2-1.3 Å2
2---7.6 Å20 Å2
3---8.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6121 0 0 0 6121
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_mcbond_it1.91.5
X-RAY DIFFRACTIONx_mcangle_it2.52
X-RAY DIFFRACTIONx_scbond_it3.42
X-RAY DIFFRACTIONx_scangle_it3.52.5
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4 136 4.5 %
Rwork0.383 2436 -
obs--85 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_mcbond_it1.91.5
X-RAY DIFFRACTIONx_scbond_it3.42
X-RAY DIFFRACTIONx_mcangle_it2.52
X-RAY DIFFRACTIONx_scangle_it3.52.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.4 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.383

+
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