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- PDB-4nkq: Structure of a Cytokine Receptor Complex -

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Basic information

Entry
Database: PDB / ID: 4nkq
TitleStructure of a Cytokine Receptor Complex
Components
  • Cytokine receptor common subunit beta
  • Granulocyte-macrophage colony-stimulating factor receptor subunit alpha
  • Granulocyte-macrophage colony-stimulating factor
KeywordsCYTOKINE/CYTOKINE RECEPTOR / GM-CSF / receptor complex / dodecamer / Disease mutation / Glycoprotein / Membrane / Phosphoprotein / Transmembrane / Cytokine / Growth factor / Secreted / CYTOKINE-CYTOKINE RECEPTOR complex
Function / homology
Function and homology information


granulocyte macrophage colony-stimulating factor receptor binding / histamine secretion / neutrophil differentiation / response to silicon dioxide / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / epithelial fluid transport / positive regulation of interleukin-23 production / regulation of circadian sleep/wake cycle, sleep / dendritic cell differentiation ...granulocyte macrophage colony-stimulating factor receptor binding / histamine secretion / neutrophil differentiation / response to silicon dioxide / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / epithelial fluid transport / positive regulation of interleukin-23 production / regulation of circadian sleep/wake cycle, sleep / dendritic cell differentiation / response to fluid shear stress / positive regulation of macrophage derived foam cell differentiation / myeloid dendritic cell differentiation / 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 / myeloid cell differentiation / positive regulation of leukocyte proliferation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-3-mediated signaling pathway / cellular response to interleukin-3 / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of podosome assembly / cytokine receptor activity / cytokine binding / Interleukin-10 signaling / cell surface receptor signaling pathway via JAK-STAT / monocyte differentiation / macrophage differentiation / immunoglobulin mediated immune response / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Interleukin-3, Interleukin-5 and GM-CSF signaling / embryonic placenta development / Interleukin receptor SHC signaling / coreceptor activity / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / signaling receptor activity / RAF/MAP kinase cascade / cellular response to lipopolysaccharide / cell population proliferation / response to lipopolysaccharide / receptor complex / positive regulation of cell migration / immune response / external side of plasma membrane / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / plasma membrane
Similarity search - Function
IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Granulocyte-macrophage colony-stimulating factor / : / Granulocyte-macrophage colony-stimulating factor / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Granulocyte-macrophage colony-stimulating factor signature. / Granulocyte-macrophage colony-simulating factor (GM-CSF) / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor, family 2, conserved site ...IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Granulocyte-macrophage colony-stimulating factor / : / Granulocyte-macrophage colony-stimulating factor / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Granulocyte-macrophage colony-stimulating factor signature. / Granulocyte-macrophage colony-simulating factor (GM-CSF) / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Short hematopoietin receptor family 1 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Interferon-alpha/beta receptor, fibronectin type III / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor receptor subunit alpha / Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å
AuthorsParker, M.W. / Broughton, S.E.
Citation
Journal: Structure / Year: 2016
Title: Conformational Changes in the GM-CSF Receptor Suggest a Molecular Mechanism for Affinity Conversion and Receptor Signaling.
Authors: Broughton, S.E. / Hercus, T.R. / Nero, T.L. / Dottore, M. / McClure, B.J. / Dhagat, U. / Taing, H. / Gorman, M.A. / King-Scott, J. / Lopez, A.F. / Parker, M.W.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2008
Title: The structure of the GM-CSF receptor complex reveals a distinct mode of cytokine receptor activation.
Authors: Hansen, G. / Hercus, T.R. / McClure, B.J. / Stomski, F.C. / Dottore, M. / Powell, J. / Ramshaw, H. / Woodcock, J.M. / Xu, Y. / Guthridge, M. / McKinstry, W.J. / Lopez, A.F. / Parker, M.W.
History
DepositionNov 13, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionSep 23, 2015ID: 3CXE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytokine receptor common subunit beta
C: Granulocyte-macrophage colony-stimulating factor
B: Granulocyte-macrophage colony-stimulating factor receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4877
Polymers96,6023
Non-polymers8854
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.656, 166.656, 213.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 47258.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RB, IL3RB, IL5RB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32927
#2: Protein Granulocyte-macrophage colony-stimulating factor / / GM-CSF / Colony-stimulating factor / CSF / Molgramostin / Sargramostim


Mass: 14492.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2, GMCSF / Production host: Escherichia coli (E. coli) / References: UniProt: P04141
#3: Protein Granulocyte-macrophage colony-stimulating factor receptor subunit alpha / / GM-CSF-R-alpha / GMCSFR-alpha / GMR-alpha / CDw116


Mass: 34850.496 Da / Num. of mol.: 1 / Mutation: N346Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RA, CSF2R, CSF2RY / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P15509
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Sequence detailsFOR CHAIN B THE IDENTITY OF THE RESIDUES 23-25, 44-50, 68-74 IS UNKNOWN. THESE RESIDUES ARE LISTED ...FOR CHAIN B THE IDENTITY OF THE RESIDUES 23-25, 44-50, 68-74 IS UNKNOWN. THESE RESIDUES ARE LISTED AS UNK (UNKNOWN RESIDUE). THE COMPLETE CRYSTALLIZED SEQUENCE IS: MLLLVTSLLLCELPHPAFLLIPEKSDLRTVAPASSLNVRFDSRTMNLSWDCQENTTFSKCF LTDKKNRVVEPRLSNNECSCTFREICLHEGVTFEVHVNTSQRGFQQKLLYPNSGREGTAAQ NFSCFIYNADLMNCTWARGPTAPRDVQYFLYIRNSKRRREIRCPYYIQDSGTHVGCHLDNL SGLTSRNYFLVNGTSREIGIQFFDSLLDTKKIERFNPPSNVTVRCNTTHCLVRWKQPRTYQ KLSYLDFQYQLDVHRKNTQPGTENLLINVSGDLENRYNFPSSEPRAKHSVKIRAADVRILN WSSWSEAIEFGSDDGNLGSVYIYVLLIVGTLVCGIVLGFLFKRFLRIQRLFPPVPQIKDKL NDNHEVEDEIIWEEFTPEEGKGYREEVLTVKEIT

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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: 4.42 Å3/Da / Density % sol: 72.19 %
Crystal growTemperature: 293 K / pH: 7
Details: 100mM HEPES buffer (pH 7.0), 6%(v/v) PEG3350, 0.2M proline, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→36.08 Å / Num. obs: 26765 / % possible obs: 99.5 % / Rmerge(I) obs: 0.077
Reflection shellResolution: 3.2→3.48 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.301→36.082 Å / SU ML: 0.44 / σ(F): 1.36 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2729 1348 5.04 %
Rwork0.2293 --
obs0.2315 26763 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.301→36.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5650 0 56 0 5706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135852
X-RAY DIFFRACTIONf_angle_d1.7677951
X-RAY DIFFRACTIONf_dihedral_angle_d16.922147
X-RAY DIFFRACTIONf_chiral_restr0.068880
X-RAY DIFFRACTIONf_plane_restr0.0091028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3011-3.4190.38081330.33032479X-RAY DIFFRACTION100
3.419-3.55580.31851320.26652505X-RAY DIFFRACTION100
3.5558-3.71750.27661420.24242478X-RAY DIFFRACTION100
3.7175-3.91330.32521280.25352510X-RAY DIFFRACTION100
3.9133-4.15810.26441310.21972522X-RAY DIFFRACTION100
4.1581-4.47860.25461300.1952519X-RAY DIFFRACTION100
4.4786-4.92830.21871380.1832552X-RAY DIFFRACTION100
4.9283-5.63910.24071450.19832555X-RAY DIFFRACTION100
5.6391-7.09580.30361370.26132602X-RAY DIFFRACTION100
7.0958-36.08420.27361320.23512693X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 51.7821 Å / Origin y: -45.5912 Å / Origin z: -32.3813 Å
111213212223313233
T0.5722 Å20.0516 Å2-0.0683 Å2-0.9332 Å20.112 Å2--0.7065 Å2
L0.7745 °2-0.1451 °2-0.7998 °2-1.131 °2-0.0369 °2--1.7719 °2
S0.0177 Å °0.2691 Å °0.0647 Å °0.249 Å °0.2258 Å °0.6201 Å °0.0382 Å °-0.7315 Å °-0.2555 Å °
Refinement TLS groupSelection details: all

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