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- PDB-4uwy: FGFR1 Apo structure -

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Basic information

Entry
Database: PDB / ID: 4uwy
TitleFGFR1 Apo structure
ComponentsFIBROBLAST GROWTH FACTOR RECEPTOR 1
KeywordsTRANSFERASE / INHIBITOR / DRUG / CANCER / FGF / RECEPTORS / GROWTH FACTORS / SIGNALLING
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 / diphosphate metabolic process / Signaling by plasma membrane FGFR1 fusions / 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 ...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 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 / cementum mineralization / vitamin D3 metabolic process / 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 / receptor-receptor interaction / Epithelial-Mesenchymal Transition (EMT) during gastrulation / positive regulation of phospholipase activity / chordate embryonic development / auditory receptor cell development / positive regulation of parathyroid hormone secretion / mesenchymal cell proliferation / paraxial mesoderm development / FGFR1b ligand binding and activation / 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 / lung-associated mesenchyme development / cell projection assembly / outer ear morphogenesis / embryonic limb morphogenesis / positive regulation of endothelial cell chemotaxis / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / ureteric bud development / middle ear morphogenesis / skeletal system morphogenesis / inner ear morphogenesis / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR1 / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / midbrain development / fibroblast growth factor binding / positive regulation of MAP kinase activity / regulation of cell differentiation / PI3K Cascade / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / cardiac muscle cell proliferation / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / cell maturation / FRS-mediated FGFR1 signaling / cellular response to fibroblast growth factor stimulus / positive regulation of neuron differentiation / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / SH2 domain binding / peptidyl-tyrosine phosphorylation / stem cell proliferation / Signal transduction by L1 / skeletal system development / stem cell differentiation / positive regulation of cell differentiation / Negative regulation of FGFR1 signaling / sensory perception of sound / positive regulation of neuron projection development / receptor protein-tyrosine kinase / neuron migration / neuron projection development / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / MAPK cascade / heparin binding / protein autophosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / cytoplasmic vesicle / protein tyrosine kinase activity / angiogenesis / gene expression / in utero embryonic development / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / postsynapse / positive regulation of MAPK cascade / positive regulation of cell population proliferation / glutamatergic synapse
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 ...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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å
AuthorsThiyagarajan, N. / Bunney, T. / Katan, M.
CitationJournal: Ebiomedicine / Year: 2015
Title: The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study
Authors: Bunney, T. / Wan, S. / Thiyagarajan, N. / Sutto, L. / Williams, S.V. / Ashford, P. / Koss, H. / Knowles, M.A. / Gervasio, F.L. / Coveney, P.V. / Katan, M.
History
DepositionAug 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,8306
Polymers70,6172
Non-polymers2124
Water2,612145
1
A: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5215
Polymers35,3091
Non-polymers2124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIBROBLAST GROWTH FACTOR RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)35,3091
Polymers35,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)211.837, 49.792, 66.054
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FIBROBLAST GROWTH FACTOR RECEPTOR 1 / FGFR-1 / BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1 / BFGFR / BFGF-R-1 / FMS-LIKE TYROSINE KINASE 2 ...FGFR-1 / BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1 / BFGFR / BFGF-R-1 / FMS-LIKE TYROSINE KINASE 2 / FLT-2 / N-SAM / PROTO-ONCOGENE C-FGR / FIBROBLAST GROWTH FACTOR 1


Mass: 35308.613 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 458-765
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PJ821 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41, LAMBDA 37
References: UniProt: P11362, receptor protein-tyrosine kinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.37 Å3/Da / Density % sol: 48.03 % / Description: NONE
Crystal growpH: 7.5
Details: 20 % PEG 5K MME, 0.1 M TRIS, PH 7.5, 0.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9773
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9773 Å / Relative weight: 1
ReflectionResolution: 2.3→27.81 Å / Num. obs: 26800 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 38.65 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / % possible all: 50

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FGI

2fgi


Resolution: 2.305→27.815 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2666 1351 5.1 %
Rwork0.2114 --
obs0.2142 26654 90.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.305→27.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 10 145 4703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054674
X-RAY DIFFRACTIONf_angle_d0.9276316
X-RAY DIFFRACTIONf_dihedral_angle_d14.3981803
X-RAY DIFFRACTIONf_chiral_restr0.038696
X-RAY DIFFRACTIONf_plane_restr0.005808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3054-2.38770.3502820.27271423X-RAY DIFFRACTION52
2.3877-2.48330.31281110.26942262X-RAY DIFFRACTION81
2.4833-2.59620.34291420.25662682X-RAY DIFFRACTION97
2.5962-2.7330.33411490.26132695X-RAY DIFFRACTION98
2.733-2.90410.31341530.25952672X-RAY DIFFRACTION98
2.9041-3.1280.31431350.25912735X-RAY DIFFRACTION98
3.128-3.44230.31651360.23272726X-RAY DIFFRACTION97
3.4423-3.93920.27681430.21742553X-RAY DIFFRACTION92
3.9392-4.95840.24141300.1682746X-RAY DIFFRACTION97
4.9584-27.81680.18731700.16612809X-RAY DIFFRACTION98

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