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- PDB-4qqt: Crystal Structure of FGF Receptor (FGFR) 4 Tyrosine Kinase Domain -

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Basic information

Entry
Database: PDB / ID: 4qqt
TitleCrystal Structure of FGF Receptor (FGFR) 4 Tyrosine Kinase Domain
ComponentsFibroblast growth factor receptor 4
KeywordsTRANSFERASE / Kinase Domain Fold / Cell Signaling / Phosphotransferase / Plasmamembrane
Function / homology
Function and homology information


FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / positive regulation of catalytic activity / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / positive regulation of DNA biosynthetic process / PI-3K cascade:FGFR4 ...FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / positive regulation of catalytic activity / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / positive regulation of DNA biosynthetic process / PI-3K cascade:FGFR4 / fibroblast growth factor binding / positive regulation of proteolysis / regulation of lipid metabolic process / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / transport vesicle / FRS-mediated FGFR4 signaling / cholesterol homeostasis / Negative regulation of FGFR4 signaling / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / GPI-linked ephrin receptor activity / transmembrane-ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / glucose homeostasis / PIP3 activates AKT signaling / heparin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein autophosphorylation / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / positive regulation of ERK1 and ERK2 cascade / receptor complex / endosome / positive regulation of cell population proliferation / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / extracellular region / ATP binding / plasma membrane
Similarity search - Function
Fibroblast growth factor receptor family / 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. ...Fibroblast growth factor receptor family / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Immunoglobulin-like domain superfamily / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
Fibroblast growth factor receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsHuang, Z. / Mohammadi, M.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: DFG-out Mode of Inhibition by an Irreversible Type-1 Inhibitor Capable of Overcoming Gate-Keeper Mutations in FGF Receptors.
Authors: Huang, Z. / Tan, L. / Wang, H. / Liu, Y. / Blais, S. / Deng, J. / Neubert, T.A. / Gray, N.S. / Li, X. / Mohammadi, M.
History
DepositionJun 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Sep 20, 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_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

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Assembly

Deposited unit
A: Fibroblast growth factor receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3203
Polymers36,1281
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.384, 61.336, 61.084
Angle α, β, γ (deg.)90.00, 99.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fibroblast growth factor receptor 4 / FGFR-4


Mass: 36127.508 Da / Num. of mol.: 1 / Fragment: Tyrosine Kinase Domain of FGF receptor 4 / Mutation: R664E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR4, JTK2, TKF / Production host: Escherichia coli (E. coli)
References: UniProt: P22455, receptor protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES, 20% (w/v) PEG 4000, 0.2 M Li2SO4 and 0.01 M Taurine, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97877 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 10, 2013
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97877 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 49375 / Num. obs: 49375 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 53.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2PSQ

2psq


Resolution: 1.501→21.506 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1997 4.05 %RANDOM
Rwork0.2216 ---
obs0.2227 49314 99.73 %-
all-49314 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.501→21.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 10 0 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052266
X-RAY DIFFRACTIONf_angle_d1.0423076
X-RAY DIFFRACTIONf_dihedral_angle_d13.854839
X-RAY DIFFRACTIONf_chiral_restr0.079339
X-RAY DIFFRACTIONf_plane_restr0.005395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5009-1.53840.23651370.20333272X-RAY DIFFRACTION97
1.5384-1.580.25311420.19653378X-RAY DIFFRACTION100
1.58-1.62650.23931410.19893355X-RAY DIFFRACTION100
1.6265-1.67890.24571420.20783352X-RAY DIFFRACTION100
1.6789-1.73890.23191440.21133391X-RAY DIFFRACTION100
1.7389-1.80850.28671420.20993371X-RAY DIFFRACTION100
1.8085-1.89080.23491410.21573343X-RAY DIFFRACTION100
1.8908-1.99040.23621440.22693393X-RAY DIFFRACTION100
1.9904-2.1150.23821440.23143403X-RAY DIFFRACTION100
2.115-2.27810.24021440.2353409X-RAY DIFFRACTION100
2.2781-2.50710.25721410.24343354X-RAY DIFFRACTION100
2.5071-2.86910.29571450.25093421X-RAY DIFFRACTION100
2.8691-3.6120.2741440.23413419X-RAY DIFFRACTION100
3.612-21.50770.21031460.19193456X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 43.7983 Å / Origin y: 7.5901 Å / Origin z: 73.0391 Å
111213212223313233
T0.08 Å2-0.0069 Å20.0071 Å2-0.0841 Å20.0077 Å2--0.0832 Å2
L0.2135 °2-0.0477 °20.1182 °2-0.3195 °2-0.0501 °2--0.3961 °2
S0.0012 Å °-0.0092 Å °-0.0026 Å °-0.0202 Å °-0.0186 Å °0.0011 Å °0.0251 Å °0.0241 Å °-0.0021 Å °
Refinement TLS groupSelection details: all

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