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- PDB-1c8p: NMR STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE COMMON BETA-CHA... -

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Entry
Database: PDB / ID: 1c8p
TitleNMR STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE COMMON BETA-CHAIN IN THE GM-CSF, IL-3 AND IL-5 RECEPTORS
ComponentsCYTOKINE RECEPTOR COMMON BETA CHAIN
KeywordsMEMBRANE PROTEIN / BETA SANDWICH / CYTOKINE RECEPTOR / FN3 DOMAIN
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 / Immunoglobulins ...: / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsMulhern, T.D. / D'Andrea, R.J. / Gaunt, C. / Vandeleur, L. / Vadas, M.A. / Lopez, A.F. / Booker, G.W. / Bagley, C.J.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The solution structure of the cytokine-binding domain of the common beta-chain of the receptors for granulocyte-macrophage colony-stimulating factor, interleukin-3 and interleukin-5.
Authors: Mulhern, T.D. / Lopez, A.F. / D'Andrea, R.J. / Gaunt, C. / Vandeleur, L. / Vadas, M.A. / Booker, G.W. / Bagley, C.J.
#1: Journal: J.Biomol.NMR / Year: 1999
Title: 1H and 15N Chemical Shift Assignments for Domain 4 of the Common Beta-Chain of the IL-3, IL-5 and GM-CSF Receptors
Authors: Mulhern, T.D. / Bagley, C.J. / Gaunt, C. / Lopez, A.F. / Vadas, M.A. / D'Andrea, R.J. / Booker, G.W.
History
DepositionOct 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2000Provider: repository / Type: Initial release
SupersessionJun 21, 2000ID: 1D4Q
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: CYTOKINE RECEPTOR COMMON BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)12,1221
Polymers12,1221
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)20 / 50LOWEST ENERGY
RepresentativeModel #1minimized average structure

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Components

#1: Protein CYTOKINE RECEPTOR COMMON BETA CHAIN


Mass: 12122.479 Da / Num. of mol.: 1 / Fragment: DOMAIN 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: HEMOPOIETIC CELLS / 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 NOESY
1222D NOESY
1313D 15N-SEPARATED NOESY
141HMQC-J
NMR detailsText: THIS STRUCTURE WAS CALCULATED USING THE ARIA METHOD

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Sample preparation

Details
Solution-IDContents
10.4MM D4BC U-15N; 10MM PHOSPHATE BUFFER;90% H2O, 10% D2O
20.4MM D4BC U-15N; 10MM PHOSPHATE BUFFER;100% D2O
Sample conditionsIonic strength: 0.06M / pH: 6.1 / Pressure: AMBIENT / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVARIAN AND ASSOCIATESprocessing
XEASY1.3.13BARTELS ET AL.data analysis
X-PLOR3.851BRUNGERstructure solution
X-PLOR3.851BRUNGERrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 1500 UNAMBIGUOUS NOE-DERIVED DISTANCE RESTRAINTS, 1034 AMBIGUOUS NOE-DERIVED DISTANCE RESTRAINTS, 42 DIHEDRAL ANGLE RESTRAINTS AND 30 DISTANCE RESTRAINTS FROM ...Details: THE STRUCTURES ARE BASED ON 1500 UNAMBIGUOUS NOE-DERIVED DISTANCE RESTRAINTS, 1034 AMBIGUOUS NOE-DERIVED DISTANCE RESTRAINTS, 42 DIHEDRAL ANGLE RESTRAINTS AND 30 DISTANCE RESTRAINTS FROM HYDROGEN BONDS. THE ARIA METHOD OF NILGES ET AL. (1997) WAS USED
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 20

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