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- PDB-4qqj: Crystal Structure of FGF Receptor (FGFR) 4 Kinase Domain Harborin... -

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Basic information

Entry
Database: PDB / ID: 4qqj
TitleCrystal Structure of FGF Receptor (FGFR) 4 Kinase Domain Harboring the V550L Gate-Keeper Mutation
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 / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / Phospholipase C-mediated cascade; FGFR4 / positive regulation of DNA biosynthetic process / positive regulation of catalytic activity ...FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / Phospholipase C-mediated cascade; FGFR4 / positive regulation of DNA biosynthetic process / positive regulation of catalytic activity / fibroblast growth factor binding / PI-3K cascade:FGFR4 / 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 / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / glucose homeostasis / heparin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein autophosphorylation / 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. / Immunoglobulin subtype ...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 / 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 / Phosphorylase Kinase; 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
Fibroblast growth factor receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.682 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 27, 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)36,3343
Polymers36,1421
Non-polymers1922
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.671, 61.472, 61.819
Angle α, β, γ (deg.)90.00, 99.43, 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: 36141.535 Da / Num. of mol.: 1 / Fragment: Kinase domain Of FGF Receptor 4 / Mutation: V550L, 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
#3: 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris (pH 7.5), 20% (w/v) PEG 1500 and 0.2 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 26, 2013
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. all: 34654 / Num. obs: 34654 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 50.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2PSQ

2psq


Resolution: 1.682→43.293 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 1980 5.77 %
Rwork0.1931 --
obs0.1946 34309 95.53 %
all-34355 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.682→43.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 10 145 2363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072270
X-RAY DIFFRACTIONf_angle_d0.9723084
X-RAY DIFFRACTIONf_dihedral_angle_d13.886842
X-RAY DIFFRACTIONf_chiral_restr0.042339
X-RAY DIFFRACTIONf_plane_restr0.005399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6821-1.72420.25291370.20742218X-RAY DIFFRACTION92
1.7242-1.77080.22891400.19142295X-RAY DIFFRACTION95
1.7708-1.82290.24141410.17312296X-RAY DIFFRACTION96
1.8229-1.88180.26031400.19762292X-RAY DIFFRACTION96
1.8818-1.9490.35381320.32692177X-RAY DIFFRACTION90
1.949-2.02710.2251430.20552318X-RAY DIFFRACTION96
2.0271-2.11930.25031360.23882227X-RAY DIFFRACTION92
2.1193-2.23110.23721410.18562310X-RAY DIFFRACTION96
2.2311-2.37080.24321420.20872308X-RAY DIFFRACTION95
2.3708-2.55390.17971440.18172337X-RAY DIFFRACTION98
2.5539-2.81080.21851440.19712368X-RAY DIFFRACTION98
2.8108-3.21750.19561450.18852381X-RAY DIFFRACTION98
3.2175-4.05320.21451450.17792349X-RAY DIFFRACTION96
4.0532-43.30760.1841500.15942453X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 43.7283 Å / Origin y: 6.721 Å / Origin z: 73.5928 Å
111213212223313233
T0.1 Å2-0.0045 Å20.005 Å2-0.0897 Å20.0016 Å2--0.0979 Å2
L0.2823 °2-0.0298 °20.1402 °2-0.1083 °2-0.0867 °2--0.281 °2
S0.0101 Å °0.0117 Å °-0.024 Å °0.0177 Å °-0.026 Å °0.0134 Å °0.0313 Å °0.0262 Å °-0.0003 Å °
Refinement TLS groupSelection details: all

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