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- PDB-1ihk: CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 9 (FGF9) -

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Basic information

Entry
Database: PDB / ID: 1ihk
TitleCRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 9 (FGF9)
ComponentsGLIA-ACTIVATING FACTOR
KeywordsHORMONE/GROWTH FACTOR / b-trefoil fold / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


regulation of timing of cell differentiation / positive regulation of activin receptor signaling pathway / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / positive regulation of reproductive process / Sertoli cell proliferation / Transcriptional regulation of testis differentiation / embryonic skeletal system development / FGFR3b ligand binding and activation / eye development / Signaling by activated point mutants of FGFR3 ...regulation of timing of cell differentiation / positive regulation of activin receptor signaling pathway / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / positive regulation of reproductive process / Sertoli cell proliferation / Transcriptional regulation of testis differentiation / embryonic skeletal system development / FGFR3b ligand binding and activation / eye development / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / embryonic digestive tract development / 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 / male sex determination / activin receptor signaling pathway / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / lung-associated mesenchyme development / positive regulation of smoothened signaling pathway / positive regulation of vascular associated smooth muscle cell migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / embryonic limb morphogenesis / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / inner ear morphogenesis / smoothened signaling pathway / negative regulation of Wnt signaling pathway / PI-3K cascade:FGFR3 / positive regulation of stem cell proliferation / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / canonical Wnt signaling pathway / fibroblast growth factor receptor signaling pathway / chondrocyte differentiation / SHC-mediated cascade:FGFR3 / vascular endothelial growth factor receptor signaling pathway / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / regulation of cell migration / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR2 in disease / substantia nigra development / Signaling by FGFR1 in disease / stem cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / animal organ morphogenesis / lung development / growth factor activity / osteoblast differentiation / protein import into nucleus / positive regulation of canonical Wnt signaling pathway / male gonad development / 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 / angiogenesis / cell differentiation / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / 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
PHOSPHATE ION / Fibroblast growth factor 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPlotnikov, A.N. / Eliseenkova, A.V. / Ibrahimi, O.A. / Lemmon, M.A. / Mohammadi, M.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of fibroblast growth factor 9 reveals regions implicated in dimerization and autoinhibition.
Authors: Plotnikov, A.N. / Eliseenkova, A.V. / Ibrahimi, O.A. / Shriver, Z. / Sasisekharan, R. / Lemmon, M.A. / Mohammadi, M.
History
DepositionApr 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: GLIA-ACTIVATING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1813
Polymers19,9921
Non-polymers1902
Water1,22568
1
A: GLIA-ACTIVATING FACTOR
hetero molecules

A: GLIA-ACTIVATING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3636
Polymers39,9832
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+3/2,-z+1/41
Unit cell
Length a, b, c (Å)87.823, 87.823, 115.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein GLIA-ACTIVATING FACTOR / FIBROBLAST GROWTH FACTOR-9 / FGF9 / GAF


Mass: 19991.541 Da / Num. of mol.: 1 / Fragment: Residues 35-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF9 / Production host: Escherichia coli (E. coli) / References: UniProt: P31371
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium phosphate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 mg/mlprotein1drop
225 mMHEPES-NaOH1drop
3150 mM1dropNaCl
42 Mammonium phosphate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 177016 / Num. obs: 177016 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.264 / % possible all: 100
Reflection
*PLUS
Num. obs: 11766 / Num. measured all: 177016
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 590 5 %random
Rwork0.203 ---
obs0.203 11575 97.9 %-
all-11575 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.383 Å20 Å20 Å2
2--0.383 Å20 Å2
3----0.767 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 10 68 1370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.5
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_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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