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- PDB-2na8: Transmembrane Structure of the Cytokine Receptor Common Subunit beta -

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Basic information

Entry
Database: PDB / ID: 2na8
TitleTransmembrane Structure of the Cytokine Receptor Common Subunit beta
ComponentsCytokine receptor common subunit beta
KeywordsMEMBRANE PROTEIN / transmembrane helix
Function / homology
Function and homology information


Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / interleukin-3-mediated signaling pathway / cellular response to interleukin-3 ...Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / interleukin-3-mediated signaling pathway / cellular response to interleukin-3 / cytokine receptor activity / cell surface receptor signaling pathway via JAK-STAT / Interleukin-3, Interleukin-5 and GM-CSF signaling / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / coreceptor activity / cytokine-mediated signaling pathway / signaling receptor activity / RAF/MAP kinase cascade / response to lipopolysaccharide / external side of plasma membrane / signal transduction / plasma membrane
Similarity search - Function
: / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model21
Model type detailsminimized average
AuthorsSchmidt, T. / Ye, F. / Situ, A.J. / An, W. / Ginsberg, M.H. / Ulmer, T.S.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Conserved Ectodomain-Transmembrane Domain Linker Motif Tunes the Allosteric Regulation of Cell Surface Receptors.
Authors: Schmidt, T. / Ye, F. / Situ, A.J. / An, W. / Ginsberg, M.H. / Ulmer, T.S.
History
DepositionDec 21, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytokine receptor common subunit beta


Theoretical massNumber of molelcules
Total (without water)5,1461
Polymers5,1461
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)21 / 21all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Cytokine receptor common subunit beta / CDw131 / GM-CSF/IL-3/IL-5 receptor common beta subunit


Mass: 5146.282 Da / Num. of mol.: 1 / Fragment: Helical transmembrane residues 432-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RB, IL3RB, IL5RB / Production host: Escherichia coli (E. coli) / References: UniProt: P32927

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D quant J correlation

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N; 80% 2H] protein, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 0.5 mM / Component: entity-1 / Isotopic labeling: [U-99% 13C; U-99% 15N; 80% 2H]
Sample conditionsIonic strength: 0.05 / pH: 7.4 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 21 / Conformers submitted total number: 21

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