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- PDB-5w59: Crystal structure of a monomeric human FGF9 in complex with the e... -

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Basic information

Entry
Database: PDB / ID: 5w59
TitleCrystal structure of a monomeric human FGF9 in complex with the ectodomain of human FGFR1c
Components
  • Fibroblast growth factor 9
  • Fibroblast growth factor receptor 1
KeywordsCYTOKINE / Growth factor / Growth Factor Receptor / ligand-receptor 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 / Sertoli cell proliferation / 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 timing of cell differentiation / positive regulation of activin receptor signaling pathway / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / Sertoli cell proliferation / 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 / Transcriptional regulation of testis differentiation / 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 / FGFR3b ligand binding and activation / embryonic skeletal system development / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / response to sodium phosphate / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / 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 / receptor-receptor interaction / auditory receptor cell development / mesenchymal cell proliferation / positive regulation of parathyroid hormone secretion / fibroblast growth factor receptor binding / paraxial mesoderm development / FGFR2c ligand binding and activation / eye development / embryonic digestive tract development / 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 / male sex determination / lung-associated mesenchyme development / activin receptor signaling pathway / cell projection assembly / positive regulation of smoothened signaling pathway / positive regulation of vascular associated smooth muscle cell migration / outer ear morphogenesis / embryonic limb morphogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of endothelial cell chemotaxis / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / ureteric bud development / skeletal system morphogenesis / middle ear morphogenesis / inner ear morphogenesis / PI-3K cascade:FGFR3 / smoothened signaling pathway / 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 / midbrain development / positive regulation of MAP kinase activity / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / regulation of cell differentiation / positive regulation of cell division / PI3K Cascade / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / canonical Wnt signaling pathway / vascular endothelial growth factor receptor signaling pathway / cardiac muscle cell proliferation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / calcium ion homeostasis / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / cell maturation / positive regulation of vascular associated smooth muscle cell proliferation / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling
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 receptor 1 / Fibroblast growth factor 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsMohammadi, M. / Ma, J. / Liu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE13686 United States
CitationJournal: Structure / Year: 2017
Title: Regulation of Receptor Binding Specificity of FGF9 by an Autoinhibitory Homodimerization.
Authors: Liu, Y. / Ma, J. / Beenken, A. / Srinivasan, L. / Eliseenkova, A.V. / Mohammadi, M.
History
DepositionJun 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor 9
B: Fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7195
Polymers45,4312
Non-polymers2883
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-60 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.159, 86.793, 136.857
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 9 / FGF-9 / Glia-activating factor / GAF / Heparin-binding growth factor 9 / HBGF-9


Mass: 19994.564 Da / Num. of mol.: 1 / Fragment: UNP residues 35-208 / Mutation: D195A/L204A/L205A
Source method: isolated from a genetically manipulated source
Details: Human FGF9 carrying D195A/L204A/L205A triple mutation in its C-terminal tail that renders the ligand monomeric
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF9 / Production host: Escherichia coli (E. coli) / References: UniProt: P31371
#2: Protein Fibroblast growth factor receptor 1 / FGFR-1 / Basic fibroblast growth factor receptor 1 / bFGF-R-1 / Fms-like tyrosine kinase 2 / FLT-2 ...FGFR-1 / Basic fibroblast growth factor receptor 1 / bFGF-R-1 / Fms-like tyrosine kinase 2 / FLT-2 / N-sam / Proto-oncogene c-Fgr


Mass: 25436.053 Da / Num. of mol.: 1
Fragment: Extracellular ligand binding domain of the "c" splice isoform (UNP residues 142-365)
Source method: isolated from a genetically manipulated source
Details: Ectodomain of human FGFR1c encompassing the membrane proximal D2 and D3 region
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR1, BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR / Production host: Escherichia coli (E. coli)
References: UniProt: P11362, receptor protein-tyrosine kinase
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris, pH 8.0, 8% w/v PEG20000, 0.3 M sodium chloride, 40 mM L-proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 14, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 18063 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.087 / Net I/σ(I): 29.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 4 / Num. unique obs: 867 / Rsym value: 0.378 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OJV

3ojv


Resolution: 2.498→29.527 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1799 9.99 %Random
Rwork0.1709 ---
obs0.176 18002 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.498→29.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 15 90 2944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082926
X-RAY DIFFRACTIONf_angle_d0.9563965
X-RAY DIFFRACTIONf_dihedral_angle_d6.9041737
X-RAY DIFFRACTIONf_chiral_restr0.056422
X-RAY DIFFRACTIONf_plane_restr0.006506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4981-2.56560.31181330.21351197X-RAY DIFFRACTION98
2.5656-2.64110.28241360.20761216X-RAY DIFFRACTION98
2.6411-2.72630.30461320.20711198X-RAY DIFFRACTION99
2.7263-2.82370.24421380.20381245X-RAY DIFFRACTION99
2.8237-2.93660.28731360.19941218X-RAY DIFFRACTION100
2.9366-3.07010.27171350.1931215X-RAY DIFFRACTION99
3.0701-3.23180.26731380.20191249X-RAY DIFFRACTION99
3.2318-3.4340.2691370.19851232X-RAY DIFFRACTION100
3.434-3.69870.22321390.17811244X-RAY DIFFRACTION100
3.6987-4.070.21031390.15291259X-RAY DIFFRACTION100
4.07-4.6570.15261420.13461278X-RAY DIFFRACTION100
4.657-5.85980.18581430.14171283X-RAY DIFFRACTION100
5.8598-29.52880.19361510.1651369X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1717-0.2697-0.41050.4969-0.3020.75890.0646-0.02160.18720.0255-0.12180.0962-0.0367-0.0212-00.2147-0.0075-0.0040.25790.03640.2935-8.58418.570248.8498
2-0.1641-0.1454-0.04741.1492-0.64920.67920.08-0.02350.034-0.0229-0.04650.02750.1030.09150.00440.1753-0.011-0.01040.25840.03660.21437.264910.011146.2327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 58 through 203)
2X-RAY DIFFRACTION2(chain 'B' and resid 147 through 360)

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