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- PDB-2lzl: FGFR3tm -

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Basic information

Entry
Database: PDB / ID: 2lzl
TitleFGFR3tm
ComponentsFibroblast growth factor receptor 3
KeywordsMEMBRANE PROTEIN / transmembrane domain / fibroblast growth factor receptor / dimerization / tyrosine kinase
Function / homology
Function and homology information


fibroblast growth factor receptor apoptotic signaling pathway / t(4;14) translocations of FGFR3 / negative regulation of developmental growth / 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 ...fibroblast growth factor receptor apoptotic signaling pathway / t(4;14) translocations of FGFR3 / negative regulation of developmental growth / 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 / fibroblast growth factor receptor activity / endochondral ossification / positive regulation of phospholipase activity / bone morphogenesis / PI-3K cascade:FGFR3 / fibroblast growth factor binding / bone mineralization / cell surface receptor signaling pathway via JAK-STAT / PI3K Cascade / fibroblast growth factor receptor signaling pathway / chondrocyte differentiation / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / positive regulation of tyrosine phosphorylation of STAT protein / transport vesicle / Signaling by FGFR3 in disease / skeletal system development / Negative regulation of FGFR3 signaling / receptor protein-tyrosine kinase / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / phosphorylation / positive regulation of cell population proliferation / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular region / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1740 / : / Fibroblast growth factor receptor 3 transmembrane domain / Fibroblast growth factor receptor family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Helix non-globular / Immunoglobulin subtype 2 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1740 / : / Fibroblast growth factor receptor 3 transmembrane domain / Fibroblast growth factor receptor family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Helix non-globular / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Special / 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 / 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
Similarity search - Domain/homology
Fibroblast growth factor receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsLesovoy, D.M. / Bocharov, E.V. / Goncharuk, S.A. / Arseniev, A.S.
CitationJournal: Structure / Year: 2013
Title: Structure of FGFR3 Transmembrane Domain Dimer: Implications for Signaling and Human Pathologies.
Authors: Bocharov, E.V. / Lesovoy, D.M. / Goncharuk, S.A. / Goncharuk, M.V. / Hristova, K. / Arseniev, A.S.
History
DepositionOct 4, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor receptor 3
B: Fibroblast growth factor receptor 3


Theoretical massNumber of molelcules
Total (without water)9,2092
Polymers9,2092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 250target function
RepresentativeModel #1fewest violations

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Components

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


Mass: 4604.325 Da / Num. of mol.: 2 / Fragment: UNP residues 357-399
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)PLYSS
References: UniProt: P22607, receptor protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: dimer of transmembrane domain of human fibroblast growth factor receptor 3
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N TROSY
1312D 1H-13C constant time HSQC aliphatic
1412D 1H-13C constant time HSQC aromatic
1513D HNCO
1613D HNCA
1713D HN(CO)CA
1813D HNHA
1913D HNHB
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
114115N,13C-F1-filtered/F3-edited-NOESY

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Sample preparation

DetailsContents: 0.75 mM [U-99% 13C; U-99% 15N] FGFR3tm, 0.75 mM FGFR3tm, 88 mM [U-99% 2H] DPC, 10 mM [U-99% 2H] SDS, 0.3 mM sodium azide, 6 mM TCEP, 5 mM citric acid, 15 mM Na2HPO4, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMFGFR3tm-1[U-99% 13C; U-99% 15N]1
0.75 mMFGFR3tm-21
88 mMDPC-3[U-99% 2H]1
10 mMSDS-4[U-99% 2H]1
0.3 mMsodium azide-51
6 mMTCEP-61
5 mMcitric acid-71
15 mMNa2HPO4-81
Sample conditionsIonic strength: 50 / pH: 5.7 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CARA1.8.4Rochus Kellerchemical shift assignment
MathematicaWolfram Researchdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 250 / Conformers submitted total number: 25

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