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- PDB-1ijt: Crystal Structure of Fibroblast Growth Factor 4 (FGF4) -

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Basic information

Entry
Database: PDB / ID: 1ijt
TitleCrystal Structure of Fibroblast Growth Factor 4 (FGF4)
Componentsfibroblast growth factor 4
KeywordsHORMONE/GROWTH FACTOR / b-trefoil fold / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


cranial suture morphogenesis / FGFRL1 modulation of FGFR1 signaling / chondroblast differentiation / apoptotic process involved in morphogenesis / Specification of the neural plate border / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / mesenchymal cell proliferation ...cranial suture morphogenesis / FGFRL1 modulation of FGFR1 signaling / chondroblast differentiation / apoptotic process involved in morphogenesis / Specification of the neural plate border / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / mesenchymal cell proliferation / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / Developmental Lineage of Pancreatic Acinar Cells / embryonic hindlimb morphogenesis / epithelial cell apoptotic process / cartilage condensation / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of stem cell proliferation / odontogenesis of dentin-containing tooth / positive regulation of cell division / PI3K Cascade / somatic stem cell population maintenance / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / neurogenesis / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / regulation of cell migration / cellular response to leukemia inhibitory factor / stem cell proliferation / Negative regulation of FGFR3 signaling / growth factor activity / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell signaling / PIP3 activates AKT signaling / heparin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytoplasm
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBellosta, P. / Plotnikov, A.N. / Eliseenkova, A.V. / Basilico, C. / Mohammadi, M.
CitationJournal: Mol.Cell.Biol. / Year: 2001
Title: Identification of receptor and heparin binding sites in fibroblast growth factor 4 by structure-based mutagenesis.
Authors: Bellosta, P. / Iwahori, A. / Plotnikov, A.N. / Eliseenkova, A.V. / Basilico, C. / Mohammadi, M.
History
DepositionApr 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fibroblast growth factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5594
Polymers14,2711
Non-polymers2883
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.367, 53.295, 56.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein fibroblast growth factor 4 / FGF4


Mass: 14270.591 Da / Num. of mol.: 1 / Fragment: b-trefoil domain / Mutation: S182G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08620
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mg/mlprotein1drop
225 mMHEPES-NaOH1drop
3150 mM1dropNaCl
430 %PEG80001reservoir
50.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9794 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 1998
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 40562 / Num. obs: 40562 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.109 / % possible all: 99.5
Reflection
*PLUS
Num. obs: 11590 / Num. measured all: 40562
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FGF

2fgf


Resolution: 1.8→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 594 5.1 %RANDOM
Rwork0.1943 ---
all-11488 --
obs-11488 97.9 %-
Solvent computationSolvent model: CNS / Bsol: 74.852 Å2 / ksol: 0.571 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.65 Å20 Å20 Å2
2--0.683 Å20 Å2
3---2.967 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 0 15 96 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004596
X-RAY DIFFRACTIONc_angle_d1.31288
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_improper_angle_d0.72077
X-RAY DIFFRACTIONc_mcbond_it0.6951.5
X-RAY DIFFRACTIONc_mcangle_it1.0942
X-RAY DIFFRACTIONc_scbond_it1.2282
X-RAY DIFFRACTIONc_scangle_it1.9392.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.31288
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72077

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