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- PDB-3f1r: Crystal structure of FGF20 dimer -

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Basic information

Entry
Database: PDB / ID: 3f1r
TitleCrystal structure of FGF20 dimer
ComponentsFibroblast growth factor 20
KeywordsHORMONE / beta-trefoil fold / Growth factor / Polymorphism / Secreted
Function / homology
Function and homology information


positive regulation of dopaminergic neuron differentiation / FGFR3 mutant receptor activation / : / inner ear receptor cell differentiation / regulation of cardiac muscle cell proliferation / FGFR3b ligand binding and activation / receptor-receptor interaction / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 ...positive regulation of dopaminergic neuron differentiation / FGFR3 mutant receptor activation / : / inner ear receptor cell differentiation / regulation of cardiac muscle cell proliferation / FGFR3b ligand binding and activation / receptor-receptor interaction / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / 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 / heparan sulfate proteoglycan binding / PI-3K cascade:FGFR3 / regulation of dopamine secretion / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / PI3K Cascade / 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 FGFR2 in disease / Signaling by FGFR1 in disease / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / growth factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / signaling receptor binding / positive regulation of cell population proliferation / signal transduction / extracellular region
Similarity search - Function
Fibroblast growth factor 20 / 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 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKalinina, J. / Mohammadi, M.
CitationJournal: Mol.Cell.Biol. / Year: 2009
Title: Homodimerization controls the fibroblast growth factor 9 subfamily's receptor binding and heparan sulfate-dependent diffusion in the extracellular matrix
Authors: Kalinina, J. / Byron, S.A. / Makarenkova, H.P. / Olsen, S.K. / Eliseenkova, A.V. / Larochelle, W.J. / Dhanabal, M. / Blais, S. / Ornitz, D.M. / Day, L.A. / Neubert, T.A. / Pollock, P.M. / Mohammadi, M.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Fibroblast growth factor 20
B: Fibroblast growth factor 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6428
Polymers47,0652
Non-polymers5766
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-79 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.144, 102.144, 119.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Fibroblast growth factor 20 / FGF-20


Mass: 23532.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF20 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: Q9NP95
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M Li2SO4, 15% Glycerol, 13% PEG 2000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2004
RadiationMonochromator: KOHZU DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→35.58 Å / Num. obs: 16050 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.056 / Net I/σ(I): 20.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.9 % / Rsym value: 0.284 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IHK

1ihk


Resolution: 2.5→35.58 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 680 -RANDOM
Rwork0.256 ---
all-14309 --
obs-14309 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-40.823 Å214.195 Å20 Å2
2--40.823 Å20 Å2
3----81.647 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 30 9 2549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.427
X-RAY DIFFRACTIONc_improper_angle_d0.772

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