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- PDB-1evt: CRYSTAL STRUCTURE OF FGF1 IN COMPLEX WITH THE EXTRACELLULAR LIGAN... -

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Basic information

Entry
Database: PDB / ID: 1evt
TitleCRYSTAL STRUCTURE OF FGF1 IN COMPLEX WITH THE EXTRACELLULAR LIGAND BINDING DOMAIN OF FGF RECEPTOR 1 (FGFR1)
Components
  • PROTEIN (FIBROBLAST GROWTH FACTOR 1)
  • PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 1)
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


Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / diphosphate metabolic process / Signaling by plasma membrane FGFR1 fusions / regulation of phosphate transport / FGFR1c and Klotho ligand binding and activation / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / diphosphate metabolic process / Signaling by plasma membrane FGFR1 fusions / regulation of phosphate transport / FGFR1c and Klotho ligand binding and activation / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / vitamin D3 metabolic process / cementum mineralization / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / regulation of endothelial cell chemotaxis to fibroblast growth factor / response to sodium phosphate / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / receptor-receptor interaction / Epithelial-Mesenchymal Transition (EMT) during gastrulation / positive regulation of phospholipase activity / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / chordate embryonic development / Phospholipase C-mediated cascade; FGFR3 / positive regulation of parathyroid hormone secretion / auditory receptor cell development / mesenchymal cell proliferation / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / paraxial mesoderm development / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / regulation of postsynaptic density assembly / Signaling by activated point mutants of FGFR1 / fibroblast growth factor receptor activity / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade: FGFR1 / lung-associated mesenchyme development / cell projection assembly / S100 protein binding / outer ear morphogenesis / embryonic limb morphogenesis / positive regulation of endothelial cell chemotaxis / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / ureteric bud development / middle ear morphogenesis / skeletal system morphogenesis / inner ear morphogenesis / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR1 / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / positive regulation of sprouting angiogenesis / midbrain development / fibroblast growth factor binding / positive regulation of MAP kinase activity / regulation of cell differentiation / positive regulation of intracellular signal transduction / positive regulation of cell division / PI3K Cascade / epithelial to mesenchymal transition / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / activation of protein kinase B activity / chondrocyte differentiation / cardiac muscle cell proliferation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / cell maturation / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / cellular response to fibroblast growth factor stimulus / neurogenesis / Signaling by FGFR2 in disease / positive regulation of neuron differentiation / Signaling by FGFR1 in disease
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic 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 / Immunoglobulin / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 ...Fibroblast growth factor receptor 1, catalytic 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 / Immunoglobulin / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 1 / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 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 20, 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 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (FIBROBLAST GROWTH FACTOR 1)
B: PROTEIN (FIBROBLAST GROWTH FACTOR 1)
C: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 1)
D: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3708
Polymers80,9864
Non-polymers3844
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-93 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.553, 64.061, 64.139
Angle α, β, γ (deg.)93.40, 111.17, 97.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PROTEIN (FIBROBLAST GROWTH FACTOR 1) / FGF1


Mass: 15232.148 Da / Num. of mol.: 2
Fragment: THE B-TREFOIL CORE OF FIBROBLAST GROWTH FACTOR 1 (FGF1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Bacteria (eubacteria) / References: UniProt: P05230
#2: Protein PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 1) / FGFR1


Mass: 25260.777 Da / Num. of mol.: 2
Fragment: EXTRACELLULAR LIGAND BINDING DOMAIN OF FGF RECEPTOR 1 (FGFR1) CONSISTING OF IMMUNOGLOBULIN LIKE DOMAINS II (D2) AND III (D3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Bacteria (eubacteria) / References: UniProt: P11362
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
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: 2.92 Å3/Da / Density % sol: 57.82 %
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
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mg/mlprotein1drop
20.1 MTris-HCl1drop
330 %PEG40001reservoir
40.2 M1reservoirLi2SO4
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9794
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 49288 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.226 / % possible all: 90.5
Reflection
*PLUS
Num. obs: 22330 / Num. measured all: 49288
Reflection shell
*PLUS
% possible obs: 90.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.8→25 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1051 -RANDOM
Rwork0.249 ---
obs0.249 21539 95.7 %-
Solvent computationSolvent model: CNS / Bsol: 27.76 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.158 Å23.159 Å2-4.057 Å2
2--1.746 Å2-3.861 Å2
3----1.588 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4963 0 20 0 4983
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.47
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_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.7591.5
X-RAY DIFFRACTIONc_mcangle_it2.8472
X-RAY DIFFRACTIONc_scbond_it2.7362
X-RAY DIFFRACTIONc_scangle_it4.0632.5
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

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