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- EMDB-41368: GM-CSF Receptor Complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41368
TitleGM-CSF Receptor Complex
Map data
Sample
  • Complex: GM-CSF Receptor Complex
    • Protein or peptide: Granulocyte-macrophage colony-stimulating factor receptor subunit alpha
    • Protein or peptide: Cytokine receptor common subunit beta
    • Protein or peptide: Granulocyte-macrophage colony-stimulating factor
KeywordsGM-CSF / cytokine / receptor / SIGNALING PROTEIN
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 / respiratory gaseous exchange by respiratory system / myeloid dendritic cell differentiation / 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 / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / 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 / Interleukin-3, Interleukin-5 and GM-CSF signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / immunoglobulin mediated immune response / 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 / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Granulocyte-macrophage colony-stimulating factor / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor signature. / Granulocyte-macrophage colony-simulating factor (GM-CSF) / Short hematopoietin receptor, family 2, conserved site ...IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Granulocyte-macrophage colony-stimulating factor / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor signature. / Granulocyte-macrophage colony-simulating factor (GM-CSF) / 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 / Four-helical cytokine-like, core / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsCaveney NA / Garcia KC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Organizing structural principles of common beta family signaling
Authors: Caveney NA / Rodriguez GE / Pollmann C / Householder KD / Saxton RA / Piehler J / Garcia KC
History
DepositionJul 26, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41368.png

Downloads & links

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Map

FileDownload / File: emd_41368.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.2364 Å
Density
Contour LevelBy AUTHOR: 0.155
Minimum - Maximum-0.061693564 - 1.596538
Average (Standard dev.)0.0007781414 (±0.02086297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 237.3888 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41368_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41368_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41368_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GM-CSF Receptor Complex

EntireName: GM-CSF Receptor Complex
Components
  • Complex: GM-CSF Receptor Complex
    • Protein or peptide: Granulocyte-macrophage colony-stimulating factor receptor subunit alpha
    • Protein or peptide: Cytokine receptor common subunit beta
    • Protein or peptide: Granulocyte-macrophage colony-stimulating factor

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Supramolecule #1: GM-CSF Receptor Complex

SupramoleculeName: GM-CSF Receptor Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Granulocyte-macrophage colony-stimulating factor receptor subunit...

MacromoleculeName: Granulocyte-macrophage colony-stimulating factor receptor subunit alpha
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKLI PEKSDLRTVA PASSLNVRFD SRTMNLSWDC QENTTFSKCF LTDKKNRVVE PRLSNNECSC TFREICLHEG VTFEVHVNTS QRGFQQKLLY PNSGREGTAA QNFSCFIYNA DLMNCTWARG PTAPRDVQYF LYIRNSKRRR EIRCPYYIQD SGTHVGCHLD ...String:
DYKDDDDKLI PEKSDLRTVA PASSLNVRFD SRTMNLSWDC QENTTFSKCF LTDKKNRVVE PRLSNNECSC TFREICLHEG VTFEVHVNTS QRGFQQKLLY PNSGREGTAA QNFSCFIYNA DLMNCTWARG PTAPRDVQYF LYIRNSKRRR EIRCPYYIQD SGTHVGCHLD NLSGLTSRNY FLVNGTSREI GIQFFDSLLD TKKIERFNPP SNVTVRCNTT HCLVRWKQPR TYQKLSYLDF QYQLDVHRKN TQPGTENLLI NVSGDLENRY NFPSSEPRAK HSVKIRAADV RILNWSSWSE AIEFGSDDGN LGGGGGSTTA PSAQLKKKLQ ALKKKNAQLK WKLQALKKKL AQGAAEDQVD PRLIDGKHHH HHHHH

UniProtKB: Granulocyte-macrophage colony-stimulating factor receptor subunit alpha

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Macromolecule #2: Cytokine receptor common subunit beta

MacromoleculeName: Cytokine receptor common subunit beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKMV SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKQH DFFKSAMPEG YVQERTIFFK DDGNYKTRAE VKFEGDTLVN RIELKGIDFK EDGNILGHKL EYNYNSHNVY IMADKQKNGI ...String:
DYKDDDDKMV SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKQH DFFKSAMPEG YVQERTIFFK DDGNYKTRAE VKFEGDTLVN RIELKGIDFK EDGNILGHKL EYNYNSHNVY IMADKQKNGI KVNFKIRHNI EDGSVQLADH YQQNTPIGDG PVLLPDNHYL STQSALSKDP NEKRDHMVLL EFVTAAGITL GMDELYKLEV LFQGPGSGAE ETIPLQTLRC YNDYTSHITC RWADTQDAQR LVNVTLIRRV NEDLLEPVSC DLSDDMPWSA CPHPRCVPRR CVIPCQSFVV TDVDYFSFQP DRPLGTRLTV TLTQHVQPPE PRDLQISTDQ DHFLLTWSVA LGSPQSHWLS PGDLEFEVVY KRLQDSWEDA AILLSNTSQA TLGPEHLMPS STYVARVRTR LAPGSRLSGR PSKWSPEVCW DSQPGDEAQP QNLECFFDGA AVLSCSWEVR KEVASSVSFG LFYKPSPDAG EEECSPVLRE GLGSLHTRHH CQIPVPDPAT HGQYIVSVQP RRAEKHIKSS VNIQMAPPSL NVTKDGDSYS LRWETMKMRY EHIDHTFEIQ YRKDTATWKD SKTETLQNAH SMALPALEPS TRYWARVRVR TSRTGYNGIW SEWSEARSWD TESVLPMGGG GSTTAPSAQL EKELQALEKE NAQLEWELQA LEKELAQ

UniProtKB: Cytokine receptor common subunit beta

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Macromolecule #3: Granulocyte-macrophage colony-stimulating factor

MacromoleculeName: Granulocyte-macrophage colony-stimulating factor / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
DYKDDDDKPA RSPSPSTQPW EHVNAIQEAR RLLNLSRDTA AEMNETVEVI SEMFDLQEPT CLQTRLELYK QGLRGSLTKL KGPLTMMASH YKQHCPPTPE TSCATQIITF ESFKENLKDF LLVIPFDCWE PVQEGAAEDQ VDPRLIDGKH HHHHHHH

UniProtKB: Granulocyte-macrophage colony-stimulating factor

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 388885
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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