[English] 日本語
Yorodumi
- PDB-1ev2: CRYSTAL STRUCTURE OF FGF2 IN COMPLEX WITH THE EXTRACELLULAR LIGAN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ev2
TitleCRYSTAL STRUCTURE OF FGF2 IN COMPLEX WITH THE EXTRACELLULAR LIGAND BINDING DOMAIN OF FGF RECEPTOR 2 (FGFR2)
Components
  • PROTEIN (FIBROBLAST GROWTH FACTOR 2)
  • PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
KeywordsGROWTH FACTOR/GROWTH FACTOR RECEPTOR / IMMUNOGLOBULIN (IG)LIKE DOMAINS BELONGING TO THE I-SET SUBGROUP WITHIN IG-LIKE DOMAINS / B-TREFOIL FOLD / GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / chondroblast differentiation / lacrimal gland development / otic vesicle formation / prostate gland morphogenesis / lymphatic endothelial cell migration / chemokine binding / regulation of smooth muscle cell differentiation / orbitofrontal cortex development / negative regulation of fibroblast growth factor receptor signaling pathway / regulation of morphogenesis of a branching structure / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / branching morphogenesis of a nerve / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / embryonic organ morphogenesis / positive regulation of cerebellar granule cell precursor proliferation / endochondral bone growth / morphogenesis of embryonic epithelium / epidermis morphogenesis / bud elongation involved in lung branching / cerebellar granule cell precursor proliferation / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / positive regulation of stem cell differentiation / membranous septum morphogenesis / reproductive structure development / limb bud formation / lung lobe morphogenesis / positive regulation of epithelial tube formation / hyaluronan catabolic process / receptor-receptor interaction / regulation of endothelial cell chemotaxis to fibroblast growth factor / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / glial cell differentiation / embryonic digestive tract morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / negative regulation of wound healing / mesenchymal cell differentiation / inner ear auditory receptor cell differentiation / stem cell development / branching involved in prostate gland morphogenesis / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / mesenchymal cell proliferation involved in lung development / Phospholipase C-mediated cascade; FGFR3 / branching involved in labyrinthine layer morphogenesis / embryonic morphogenesis / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / mammary gland epithelial cell differentiation / Phospholipase C-mediated cascade; FGFR4 / embryonic pattern specification / outflow tract septum morphogenesis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / paracrine signaling / mesodermal cell differentiation / negative regulation of fibroblast migration / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / digestive tract development / cell migration involved in sprouting angiogenesis
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil ...HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Fibroblast growth factor 2 / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsPlotnikov, A.N. / Hubbard, S.R. / Schlessinger, J. / Mohammadi, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal structures of two FGF-FGFR complexes reveal the determinants of ligand-receptor specificity.
Authors: Plotnikov, A.N. / Hubbard, S.R. / Schlessinger, J. / Mohammadi, M.
History
DepositionApr 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (FIBROBLAST GROWTH FACTOR 2)
B: PROTEIN (FIBROBLAST GROWTH FACTOR 2)
C: PROTEIN (FIBROBLAST GROWTH FACTOR 2)
D: PROTEIN (FIBROBLAST GROWTH FACTOR 2)
E: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
F: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
G: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
H: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,38912
Polymers159,0058
Non-polymers3844
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.198, 71.677, 90.920
Angle α, β, γ (deg.)90.53, 89.98, 89.99
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
PROTEIN (FIBROBLAST GROWTH FACTOR 2) / FGF2


Mass: 15110.339 Da / Num. of mol.: 4 / Fragment: THE B-TREFOIL CORE OF FIBROBLAST GROWTH FACTOR 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P09038
#2: Protein
PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2) / FGFR2


Mass: 24640.934 Da / Num. of mol.: 4
Fragment: EXTRACELLULAR LIGAND BINDING DOMAIN OF FGF RECEPTOR 2 CONSISTING OF IMMUNOGLOBULIN LIKE DOMAINS II (D2) AND III (D3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: P21802
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG 4000, Isopropanol, HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 mMTris-HCl1drop
3150 mM1dropNaCl
410-15 %PEG40001reservoir
510 %isopropanol1reservoir
60.1 MHEPES-NaOH1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9789
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Sep 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 206913 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.241 / % possible all: 87.8
Reflection
*PLUS
Num. obs: 93440 / Num. measured all: 206913
Reflection shell
*PLUS
% possible obs: 87.8 %

-
Processing

Software
NameClassification
SDMSdata collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
SDMSdata reduction
RefinementResolution: 2.2→25 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.273 4291 -RANDOM
Rwork0.248 ---
obs0.248 84816 91.7 %-
Solvent computationSolvent model: CNS / Bsol: 47.84 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.903 Å20 Å20 Å2
2---0.988 Å2-0.658 Å2
3---15.892 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9818 0 20 263 10101
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.33
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.782
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.8711.5
X-RAY DIFFRACTIONc_mcangle_it1.5322
X-RAY DIFFRACTIONc_scbond_it1.1552
X-RAY DIFFRACTIONc_scangle_it1.7882.5
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.782

+
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