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- PDB-1cvs: CRYSTAL STRUCTURE OF A DIMERIC FGF2-FGFR1 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1cvs
TitleCRYSTAL STRUCTURE OF A DIMERIC FGF2-FGFR1 COMPLEX
Components
  • FIBROBLAST GROWTH FACTOR 2Basic fibroblast growth factor
  • FIBROBLAST GROWTH FACTOR RECEPTOR 1
KeywordsGROWTH FACTOR/GROWTH FACTOR RECEPTOR / FGF / FGFR / IMMUNOGLOBULIN-LIKE / SIGNAL TRANSDUCTION / DIMERIZATION / GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / chondroblast differentiation / lymphatic endothelial cell migration / chemokine binding / negative regulation of 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 / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / positive regulation of cerebellar granule cell precursor proliferation / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / cementum mineralization / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / cerebellar granule cell precursor proliferation / receptor-receptor interaction / positive regulation of stem cell differentiation / response to sodium phosphate / hyaluronan catabolic process / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / auditory receptor cell development / glial cell differentiation / ventricular zone neuroblast division / regulation of endothelial cell chemotaxis to fibroblast growth factor / Epithelial-Mesenchymal Transition (EMT) during gastrulation / inner ear auditory receptor cell differentiation / negative regulation of wound healing / positive regulation of parathyroid hormone secretion / chordate embryonic development / stem cell development / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / mesenchymal cell proliferation / embryonic morphogenesis / FGFR2b ligand binding and activation / paraxial mesoderm development / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / positive regulation of epithelial tube formation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / FGFR1b ligand binding and activation / branching involved in salivary gland morphogenesis / mammary gland epithelial cell differentiation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / paracrine signaling / lung-associated mesenchyme development / cell projection assembly / negative regulation of fibroblast migration / positive regulation of endothelial cell chemotaxis / phosphatidylinositol-mediated signaling / endothelial cell proliferation / cell migration involved in sprouting angiogenesis / outer ear morphogenesis / middle ear morphogenesis / embryonic limb morphogenesis / skeletal system morphogenesis / embryo development ending in birth or egg hatching / ureteric bud development / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / inner ear morphogenesis / Signaling by FGFR2 IIIa TM / positive regulation of DNA biosynthetic process / Syndecan interactions / midbrain development / branching involved in ureteric bud morphogenesis / positive regulation of neuroblast proliferation / positive regulation of cell migration involved in sprouting angiogenesis / PI-3K cascade:FGFR3 / fibroblast growth factor binding
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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 2 / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMEN / Resolution: 2.8 Å
AuthorsPlotnikov, A.N. / Schlessinger, J. / Hubbard, S.R. / Mohammadi, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structural basis for FGF receptor dimerization and activation.
Authors: Plotnikov, A.N. / Schlessinger, J. / Hubbard, S.R. / Mohammadi, M.
History
DepositionAug 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBROBLAST GROWTH FACTOR 2
B: FIBROBLAST GROWTH FACTOR 2
C: FIBROBLAST GROWTH FACTOR RECEPTOR 1
D: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1558
Polymers80,7704
Non-polymers3844
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-87 kcal/mol
Surface area29120 Å2
MethodPISA
2
A: FIBROBLAST GROWTH FACTOR 2
B: FIBROBLAST GROWTH FACTOR 2
C: FIBROBLAST GROWTH FACTOR RECEPTOR 1
D: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules

A: FIBROBLAST GROWTH FACTOR 2
B: FIBROBLAST GROWTH FACTOR 2
C: FIBROBLAST GROWTH FACTOR RECEPTOR 1
D: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,30916
Polymers161,5418
Non-polymers7698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Buried area20450 Å2
ΔGint-193 kcal/mol
Surface area53730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.450, 98.450, 197.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FIBROBLAST GROWTH FACTOR 2 / Basic fibroblast growth factor


Mass: 15110.339 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P09038
#2: Protein FIBROBLAST GROWTH FACTOR RECEPTOR 1 /


Mass: 25274.805 Da / Num. of mol.: 2 / Fragment: IG-LIKE DOMAINS 2 AND 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P11362
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, glycerol, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 mMTris-HCl1drop
3150 mM1dropNaCl
41.6 Mammonium sulfate1reservoir
520 %glycerol1reservoir
60.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.984
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Apr 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 196126 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.255 / % possible all: 98.1
Reflection
*PLUS
Num. obs: 24726 / Num. measured all: 196126
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameClassification
SDMSdata collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
SDMSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMEN
Starting model: FGF2, TELOKIN

Resolution: 2.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1143 4.6 %RANDOM
Rwork0.24 ---
obs0.24 23830 96.9 %-
Solvent computationSolvent model: CNS / Bsol: 27 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1--9.08 Å20 Å20 Å2
2---9.08 Å20 Å2
3---18.17 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5153 0 20 0 5173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.45
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_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.112.5
Refine LS restraints NCSNCS model details: RESTRAINED
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93

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