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- PDB-1ev2: CRYSTAL STRUCTURE OF FGF2 IN COMPLEX WITH THE EXTRACELLULAR LIGAN... -

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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 / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of cell fate specification / regulation of cell migration involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / response to wortmannin / Formation of intermediate mesoderm / chondroblast differentiation ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of cell fate specification / regulation of cell migration involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / response to wortmannin / Formation of intermediate mesoderm / chondroblast differentiation / FGFRL1 modulation of FGFR1 signaling / 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 / negative regulation of fibroblast growth factor receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / prostate gland morphogenesis / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / lacrimal gland development / otic vesicle formation / bud elongation involved in lung branching / regulation of smooth muscle cell differentiation / prostate epithelial cord elongation / stem cell development / lung lobe morphogenesis / regulation of morphogenesis of a branching structure / epithelial cell proliferation involved in salivary gland morphogenesis / chemokine binding / branching involved in labyrinthine layer morphogenesis / orbitofrontal cortex development / morphogenesis of embryonic epithelium / branching involved in salivary gland morphogenesis / mesenchymal cell proliferation involved in lung development / lung-associated mesenchyme development / epidermis morphogenesis / branching morphogenesis of a nerve / gland morphogenesis / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / embryonic organ morphogenesis / limb bud formation / endochondral bone growth / membranous septum morphogenesis / reproductive structure development / embryonic digestive tract morphogenesis / angiogenesis involved in coronary vascular morphogenesis / Formation of the nephric duct / positive regulation of epithelial cell proliferation involved in lung morphogenesis / regulation of endothelial cell chemotaxis to fibroblast growth factor / organ growth / branching involved in prostate gland morphogenesis / negative regulation of fibroblast migration / negative regulation of wound healing / mesenchymal cell differentiation / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / receptor-receptor interaction / fibroblast growth factor receptor binding / hyaluronan catabolic process / FGFR2b ligand binding and activation / positive regulation of phospholipase activity / positive regulation of mesenchymal cell proliferation / embryonic morphogenesis / FGFR4 ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / positive regulation of epithelial tube formation / lung alveolus development / Phospholipase C-mediated cascade; FGFR2 / Phospholipase C-mediated cascade; FGFR4 / FGFR1b ligand binding and activation / embryonic cranial skeleton morphogenesis / regulation of osteoblast proliferation / Signaling by activated point mutants of FGFR1 / stem cell proliferation / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / fibroblast growth factor receptor activity / embryonic pattern specification / pyramidal neuron development / cell migration involved in sprouting angiogenesis / ureteric bud development / negative regulation of keratinocyte proliferation / embryo development ending in birth or egg hatching / outflow tract septum morphogenesis / paracrine signaling / regulation of smoothened signaling pathway / hair follicle morphogenesis / skeletal system morphogenesis / behavioral response to ethanol
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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin domain ...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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin domain / 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 / 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
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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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 %

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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

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