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- PDB-2l6w: PDGFR beta-TM -

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Basic information

Entry
Database: PDB / ID: 2l6w
TitlePDGFR beta-TM
ComponentsBeta-type platelet-derived growth factor receptor
KeywordsMEMBRANE PROTEIN / transmembrane helix / receptor tyrosine kinase / heptad repeat
Function / homology
Function and homology information


platelet activating factor receptor activity / platelet-derived growth factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / metanephric glomerular capillary formation / cell migration involved in vasculogenesis / aorta morphogenesis ...platelet activating factor receptor activity / platelet-derived growth factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / metanephric glomerular capillary formation / cell migration involved in vasculogenesis / aorta morphogenesis / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / platelet-derived growth factor binding / retina vasculature development in camera-type eye / vascular endothelial growth factor binding / cardiac myofibril assembly / phosphatidylinositol metabolic process / positive regulation of chemotaxis / Signaling by PDGF / platelet-derived growth factor receptor binding / positive regulation of DNA biosynthetic process / positive regulation of smooth muscle cell migration / positive regulation of calcium ion import / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of phosphoprotein phosphatase activity / platelet-derived growth factor receptor signaling pathway / positive regulation of phospholipase C activity / positive regulation of calcium-mediated signaling / cell chemotaxis / Downstream signal transduction / lysosomal lumen / positive regulation of mitotic nuclear division / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of reactive oxygen species metabolic process / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / protein kinase activity / positive regulation of cell migration / apical plasma membrane / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / protein kinase binding / Golgi apparatus / enzyme binding / signal transduction / ATP binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Platelet-derived growth factor receptor beta / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Platelet-derived growth factor receptor beta / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin 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 / 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
Platelet-derived growth factor receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsMuhle-Goll, C. / Hoffmann, S. / Ulrich, A.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Hydrophobic matching controls the tilt and stability of the dimeric platelet-derived growth factor receptor (PDGFR) beta transmembrane segment.
Authors: Muhle-Goll, C. / Hoffmann, S. / Afonin, S. / Grage, S.L. / Polyansky, A.A. / Windisch, D. / Zeitler, M. / Burck, J. / Ulrich, A.S.
History
DepositionNov 29, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-type platelet-derived growth factor receptor
B: Beta-type platelet-derived growth factor receptor


Theoretical massNumber of molelcules
Total (without water)8,8432
Polymers8,8432
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Beta-type platelet-derived growth factor receptor / PDGF-R-beta / CD140 antigen-like family member B


Mass: 4421.528 Da / Num. of mol.: 2 / Fragment: UNP residues 526-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDGFRB / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21
References: UniProt: P09619, receptor protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: transmembrane helix of the platelet derived growth factor receptor beta
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N TOCSY
1213D 1H-15N NOESY
2313D 1H-15N NOESY
1423D HN(CA)CB
1523D HNCA
1623D CBCA(CO)NH
1723D C(CO)NH
1843D 1H-13C NOESY
2943D 1H-13C NOESY
21033D 13C-filtered 13C-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] PDGFR-TM, 200 mM [U-2H] DPC, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] PDGFR-TM, 200 mM [U-2H] DPC, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] and natural abundance PDGFR-TM, 200 mM DPC, 100% D2O100% D2O
41 mM [U-100% 13C; U-100% 15N] PDGFR-TM, 200 mM [U-2H] DPC, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPDGFR-TM-1[U-100% 15N]1
200 mMDPC-2[U-2H]1
1 mMPDGFR-TM-3[U-100% 13C; U-100% 15N]2
200 mMDPC-4[U-2H]2
1 mMPDGFR-TM-5[U-100% 13C; U-100% 15N] and natural abundance3
200 mMDPC-63
1 mMPDGFR-TM-7[U-100% 13C; U-100% 15N]4
200 mMDPC-8[U-2H]4
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1120 6.8 ambient 323 K
2120 6.8 ambient 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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