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- PDB-1fgi: CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF FIBROBLAST GRO... -

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Basic information

Entry
Database: PDB / ID: 1fgi
TitleCRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF FIBROBLAST GROWTH FACTOR RECEPTOR 1 IN COMPLEX WITH SU5402 INHIBITOR
ComponentsFGF RECEPTOR 1Fibroblast growth factor receptor
KeywordsPROTEIN KINASE / TRANSFERASE / TYROSINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / INHIBITOR
Function / homology
Function and homology information


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 / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification ...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 / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / cementum mineralization / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / receptor-receptor interaction / response to sodium phosphate / 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 / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / positive regulation of parathyroid hormone secretion / chordate embryonic development / mesenchymal cell proliferation / paraxial mesoderm development / fibroblast growth factor receptor activity / FGFR1b ligand binding and activation / branching involved in salivary gland morphogenesis / 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 / lung-associated mesenchyme development / cell projection assembly / phosphatidylinositol-mediated signaling / outer ear morphogenesis / middle ear morphogenesis / embryonic limb morphogenesis / skeletal system morphogenesis / ureteric bud development / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / inner ear morphogenesis / midbrain development / fibroblast growth factor binding / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / regulation of cell differentiation / PI-3K cascade:FGFR1 / PI3K Cascade / epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / calcium ion homeostasis / chondrocyte differentiation / positive regulation of phospholipase C activity / SHC-mediated cascade:FGFR1 / cell maturation / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR1 signaling / positive regulation of neuron differentiation / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / SH2 domain binding / Signal transduction by L1 / skeletal system development / stem cell proliferation / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / neuron migration / positive regulation of MAP kinase activity / positive regulation of neuron projection development / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / neuron projection development / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / cell migration / PIP3 activates AKT signaling / heparin binding / gene expression / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / angiogenesis / protein tyrosine kinase activity / in utero embryonic development / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein phosphorylation / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / 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 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-SU1 / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.5 Å
AuthorsMohammadi, M. / Schlessinger, J. / Hubbard, S.R.
Citation
Journal: Science / Year: 1997
Title: Structures of the tyrosine kinase domain of fibroblast growth factor receptor in complex with inhibitors.
Authors: Mohammadi, M. / McMahon, G. / Sun, L. / Tang, C. / Hirth, P. / Yeh, B.K. / Hubbard, S.R. / Schlessinger, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Structure of the Fgf Receptor Tyrosine Kinase Domain Reveals a Novel Autoinhibitory Mechanism
Authors: Mohammadi, M. / Schlessinger, J. / Hubbard, S.R.
History
DepositionMar 22, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FGF RECEPTOR 1
B: FGF RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2104
Polymers70,6172
Non-polymers5932
Water4,125229
1
A: FGF RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6052
Polymers35,3091
Non-polymers2961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FGF RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6052
Polymers35,3091
Non-polymers2961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.490, 57.790, 65.530
Angle α, β, γ (deg.)90.00, 107.68, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9944, -0.09773, 0.04029), (-0.10388, 0.83277, -0.54379), (0.01959, -0.54493, -0.83826)
Vector: 72.518, 12.243, 28.159)

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Components

#1: Protein FGF RECEPTOR 1 / Fibroblast growth factor receptor / FGFR1K


Mass: 35308.613 Da / Num. of mol.: 2 / Fragment: TYROSINE KINASE DOMAIN / Mutation: L457V, C488A, C584S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Cellular location: CYTOPLASM / Organelle: CYTOPLASM / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11362, EC: 2.7.1.112
#2: Chemical ChemComp-SU1 / 3-[(3-(2-CARBOXYETHYL)-4-METHYLPYRROL-2-YL)METHYLENE]-2-INDOLINONE / SU5402


Mass: 296.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16N2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.68 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.5
Details: 16% PEG 10000, 0.3 M (NH4)2SO4, 100 MM BIS-TRIS, PH 6.5, 5% ETHYLENE GLYCOL
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: Mohammadi, M., (1996) Cell(Cambridge,Mass.), 86, 577.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-50 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mM1dropNaCl
42 mMdithiothreitol1drop
516 %PEG100001reservoir
60.3 Mammonium sulfate1reservoir
75 %ethylene glycol1reservoir
8100 mMbis-Tris1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1996 / Details: YALE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 25350 / % possible obs: 97.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.8
Reflection
*PLUS
Num. measured all: 93535
Reflection shell
*PLUS
% possible obs: 96.1 % / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3.44refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 2.5→6 Å / Rfactor Rfree error: 0.0086 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.27 994 4.1 %RANDOM
Rwork0.19 ---
obs0.19 20402 84.6 %-
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.74 Å20 Å25.25 Å2
2---9.97 Å20 Å2
3---3.23 Å2
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 0 44 229 4636
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.071
X-RAY DIFFRACTIONx_mcangle_it1.331.5
X-RAY DIFFRACTIONx_scbond_it21.5
X-RAY DIFFRACTIONx_scangle_it2.252
Refine LS restraints NCSNCS model details: UNRESTRAINED
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPHCSDX.MISC
Software
*PLUS
Name: X-PLOR / Version: 3.44 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26

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