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- PDB-4k33: Crystal Structure of FGF Receptor 3 (FGFR3) Kinase Domain Harbori... -

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Basic information

Entry
Database: PDB / ID: 4k33
TitleCrystal Structure of FGF Receptor 3 (FGFR3) Kinase Domain Harboring the K650E Mutation, a Gain-of-Function Mutation Responsible for Thanatophoric Dysplasia Type II and Spermatocytic Seminoma
ComponentsFibroblast growth factor receptor 3
KeywordsTRANSFERASE / Kinase Domain Fold Consisting of N- and C-lobes / Receptor Tyrosine Kinase
Function / homology
Function and homology information


t(4;14) translocations of FGFR3 / negative regulation of developmental growth / fibroblast growth factor receptor apoptotic signaling pathway / Signaling by FGFR3 fusions in cancer / bone maturation / chondrocyte proliferation / endochondral bone growth / FGFR3b ligand binding and activation / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation ...t(4;14) translocations of FGFR3 / negative regulation of developmental growth / fibroblast growth factor receptor apoptotic signaling pathway / Signaling by FGFR3 fusions in cancer / bone maturation / chondrocyte proliferation / endochondral bone growth / FGFR3b ligand binding and activation / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / endochondral ossification / positive regulation of phospholipase activity / bone morphogenesis / positive regulation of tyrosine phosphorylation of STAT protein / PI-3K cascade:FGFR3 / bone mineralization / fibroblast growth factor binding / PI3K Cascade / cell surface receptor signaling pathway via JAK-STAT / fibroblast growth factor receptor signaling pathway / chondrocyte differentiation / SHC-mediated cascade:FGFR3 / transport vesicle / FRS-mediated FGFR3 signaling / Signaling by FGFR3 in disease / skeletal system development / Negative regulation of FGFR3 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 / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / stem cell 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 / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / cell-cell signaling / PIP3 activates AKT signaling / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of cell population proliferation / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular region / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Fibroblast growth factor receptor 3 transmembrane domain / 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 ...Fibroblast growth factor receptor 3 transmembrane domain / 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. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Fibroblast growth factor receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3405 Å
AuthorsHuang, Z. / Chen, H. / Mohammadi, M.
CitationJournal: Structure / Year: 2013
Title: Structural Mimicry of A-Loop Tyrosine Phosphorylation by a Pathogenic FGF Receptor 3 Mutation.
Authors: Huang, Z. / Chen, H. / Blais, S. / Neubert, T.A. / Li, X. / Mohammadi, M.
History
DepositionApr 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Dec 28, 2016Group: Structure summary
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2234
Polymers36,6691
Non-polymers5543
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.226, 61.427, 100.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fibroblast growth factor receptor 3 / FGFR-3


Mass: 36668.984 Da / Num. of mol.: 1 / Fragment: Human FGF Receptor 3 Kinase Domain / Mutation: C482A, C582S, K650E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR3, JTK4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys-S
References: UniProt: P22607, receptor protein-tyrosine kinase
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES pH7.5, 19% PEG 4000, 4% C4H10O2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 8, 2012
RadiationMonochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. all: 14385 / Num. obs: 14385 / % possible obs: 97 % / Redundancy: 4.7 % / Rsym value: 0.071 / Net I/σ(I): 32.4
Reflection shellResolution: 2.34→2.39 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.243 / % possible all: 61.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PVY

2pvy


Resolution: 2.3405→47.74 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 1435 10 %
Rwork0.1755 --
obs0.1807 14345 97.27 %
all-14385 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3405→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 33 124 2473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082407
X-RAY DIFFRACTIONf_angle_d1.1823267
X-RAY DIFFRACTIONf_dihedral_angle_d15.051909
X-RAY DIFFRACTIONf_chiral_restr0.081362
X-RAY DIFFRACTIONf_plane_restr0.006413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3405-2.42410.27941170.20451053X-RAY DIFFRACTION81
2.4241-2.52120.28231410.19261267X-RAY DIFFRACTION98
2.5212-2.63590.2991440.1991300X-RAY DIFFRACTION99
2.6359-2.77490.24941450.18961296X-RAY DIFFRACTION100
2.7749-2.94870.25791460.19571322X-RAY DIFFRACTION100
2.9487-3.17630.25411460.18181315X-RAY DIFFRACTION100
3.1763-3.49590.22571470.18791313X-RAY DIFFRACTION100
3.4959-4.00150.22661470.15951333X-RAY DIFFRACTION100
4.0015-5.04060.20441510.15341359X-RAY DIFFRACTION100
5.0406-47.75010.19651510.17821352X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 18.6536 Å / Origin y: 0.2212 Å / Origin z: 36.811 Å
111213212223313233
T0.2298 Å2-0.0082 Å20.0017 Å2-0.2364 Å2-0.0066 Å2--0.1513 Å2
L1.3433 °20.2199 °2-0.0268 °2-2.6873 °20.9862 °2--2.3776 °2
S-0.025 Å °-0.0069 Å °0.0336 Å °0.0822 Å °-0.0336 Å °0.1632 Å °-0.0556 Å °-0.1946 Å °0.0476 Å °
Refinement TLS groupSelection details: all

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