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- EMDB-39029: Structure of the ige-fc bound to its high affinity receptor fc(ep... -

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Entry
Database: EMDB / ID: EMD-39029
TitleStructure of the ige-fc bound to its high affinity receptor fc(epsilon)ri
Map data
Sample
  • Complex: Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit alpha
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit beta
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit gamma
    • Protein or peptide: Immunoglobulin heavy constant epsilon
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
Keywordscomplex / antibody / IMMUNE SYSTEM
Function / homology
Function and homology information


Fc epsilon receptor (FCERI) signaling / FCERI mediated NF-kB activation / Dectin-2 family / Role of LAT2/NTAL/LAB on calcium mobilization / Platelet Adhesion to exposed collagen / serotonin secretion / GPVI-mediated activation cascade / Cell surface interactions at the vascular wall / IgE receptor activity / Fc-epsilon receptor I complex ...Fc epsilon receptor (FCERI) signaling / FCERI mediated NF-kB activation / Dectin-2 family / Role of LAT2/NTAL/LAB on calcium mobilization / Platelet Adhesion to exposed collagen / serotonin secretion / GPVI-mediated activation cascade / Cell surface interactions at the vascular wall / IgE receptor activity / Fc-epsilon receptor I complex / FCERI mediated Ca+2 mobilization / negative regulation of mast cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / high-affinity IgE receptor activity / IgE B cell receptor complex / type I hypersensitivity / mast cell apoptotic process / mast cell activation / Fc-gamma receptor III complex / FCERI mediated MAPK activation / positive regulation of interleukin-3 production / serotonin secretion by platelet / eosinophil degranulation / neutrophil activation involved in immune response / positive regulation of mast cell cytokine production / positive regulation of mast cell degranulation / positive regulation of type III hypersensitivity / Fc-gamma receptor signaling pathway / regulation of platelet activation / IgE binding / positive regulation of type IIa hypersensitivity / type 2 immune response / regulation of release of sequestered calcium ion into cytosol / positive regulation of protein localization to cell surface / leukotriene biosynthetic process / positive regulation of type I hypersensitivity / : / interleukin-3-mediated signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / IgG binding / Neutrophil degranulation / phagocytosis, engulfment / mast cell degranulation / positive regulation of interleukin-4 production / antigen processing and presentation of exogenous peptide antigen via MHC class I / Fc-epsilon receptor signaling pathway / positive regulation of interleukin-10 production / cellular response to low-density lipoprotein particle stimulus / regulation of immune response / immunoglobulin mediated immune response / positive regulation of phagocytosis / neutrophil chemotaxis / positive regulation of calcium-mediated signaling / SH2 domain binding / osteoclast differentiation / B cell differentiation / protein localization to plasma membrane / integrin-mediated signaling pathway / establishment of localization in cell / phosphoprotein binding / B cell receptor signaling pathway / calcium-mediated signaling / receptor internalization / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of interleukin-6 production / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / positive regulation of tumor necrosis factor production / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / cell surface receptor signaling pathway / endosome / defense response to bacterium / immune response / protein heterodimerization activity / external side of plasma membrane / lysosomal membrane / innate immune response / protein kinase binding / cell surface / signal transduction / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
High affinity immunoglobulin epsilon receptor subunit gamma / Membrane-spanning 4-domains subfamily A / CD20-like family / CD20-like family / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / : / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. ...High affinity immunoglobulin epsilon receptor subunit gamma / Membrane-spanning 4-domains subfamily A / CD20-like family / CD20-like family / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / : / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant epsilon / High affinity immunoglobulin epsilon receptor subunit alpha / High affinity immunoglobulin epsilon receptor subunit beta / High affinity immunoglobulin epsilon receptor subunit gamma
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsDu S / Deng MJ / Xiao JY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2024
Title: Structural insights into the high-affinity IgE receptor FcεRI complex.
Authors: Meijie Deng / Shuo Du / Handi Hou / Junyu Xiao /
Abstract: Immunoglobulin E (IgE) plays a pivotal role in allergic responses. The high-affinity IgE receptor, FcεRI, found on mast cells and basophils, is central to the effector functions of IgE. FcεRI is a ...Immunoglobulin E (IgE) plays a pivotal role in allergic responses. The high-affinity IgE receptor, FcεRI, found on mast cells and basophils, is central to the effector functions of IgE. FcεRI is a tetrameric complex, comprising FcεRIα, FcεRIβ and a homodimer of FcRγ (originally known as FcεRIγ), with FcεRIα recognizing the Fc region of IgE (Fcε) and FcεRIβ-FcRγ facilitating signal transduction. Additionally, FcRγ is a crucial component of other immunoglobulin receptors, including those for IgG (FcγRI and FcγRIIIA) and IgA (FcαRI). However, the molecular basis of FcεRI assembly and the structure of FcRγ have remained elusive. Here we elucidate the cryogenic electron microscopy structure of the Fcε-FcεRI complex. FcεRIα has an essential role in the receptor's assembly, interacting with FcεRIβ and both FcRγ subunits. FcεRIβ is structured as a compact four-helix bundle, similar to the B cell antigen CD20. The FcRγ dimer exhibits an asymmetric architecture, and coils with the transmembrane region of FcεRIα to form a three-helix bundle. A cholesterol-like molecule enhances the interaction between FcεRIβ and the FcεRIα-FcRγ complex. Our mutagenesis analyses further indicate similarities between the interaction of FcRγ with FcεRIα and FcγRIIIA, but differences in that with FcαRI. These findings deepen our understanding of the signalling mechanisms of FcεRI and offer insights into the functionality of other immune receptors dependent on FcRγ.
History
DepositionFeb 5, 2024-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39029.png

Downloads & links

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Map

FileDownload / File: emd_39029.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.5962684 - 3.6380997
Average (Standard dev.)-0.0007991625 (±0.058081258)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39029_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_39029_half_map_2.map
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Sample components

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Entire : Structure of the ige-fc bound to its high affinity receptor fc(ep...

EntireName: Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri
Components
  • Complex: Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit alpha
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit beta
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit gamma
    • Protein or peptide: Immunoglobulin heavy constant epsilon
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Structure of the ige-fc bound to its high affinity receptor fc(ep...

SupramoleculeName: Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: High affinity immunoglobulin epsilon receptor subunit alpha

MacromoleculeName: High affinity immunoglobulin epsilon receptor subunit alpha
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 27.83016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDTGGSARLC LALVLISLGV MLTATQKSVV SLDPPWIRIL TGDKVTLICN GNNSSQMNST KWIHNDSISN VKSSHWVIVS ATIQDSGKY ICQKQGFYKS KPVYLNVMQE WLLLQSSADV VLDNGSFDIR CRSWKKWKVH KVIYYKDDIA FKYSYDSNNI S IRKATFND ...String:
MDTGGSARLC LALVLISLGV MLTATQKSVV SLDPPWIRIL TGDKVTLICN GNNSSQMNST KWIHNDSISN VKSSHWVIVS ATIQDSGKY ICQKQGFYKS KPVYLNVMQE WLLLQSSADV VLDNGSFDIR CRSWKKWKVH KVIYYKDDIA FKYSYDSNNI S IRKATFND SGSYHCTGYL NKVECKSDKF SIAVVKDYTI EYRWLQLIFP SLAVILFAVD TGLWFSTHKQ FESILKIQKT GK GKKKG

UniProtKB: High affinity immunoglobulin epsilon receptor subunit alpha

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Macromolecule #2: High affinity immunoglobulin epsilon receptor subunit beta

MacromoleculeName: High affinity immunoglobulin epsilon receptor subunit beta
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 26.747752 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDTENKSRAD LALPNPQESP SAPDIELLEA SPPAKALPEK PASPPPQQTW QSFLKKELEF LGVTQVLVGL ICLCFGTVVC STLQTSDFD DEVLLLYRAG YPFWGAVLFV LSGFLSIMSE RKNTLYLVRG SLGANIVSSI AAGLGIAILI LNLSNNSAYM N YCKDITED ...String:
MDTENKSRAD LALPNPQESP SAPDIELLEA SPPAKALPEK PASPPPQQTW QSFLKKELEF LGVTQVLVGL ICLCFGTVVC STLQTSDFD DEVLLLYRAG YPFWGAVLFV LSGFLSIMSE RKNTLYLVRG SLGANIVSSI AAGLGIAILI LNLSNNSAYM N YCKDITED DGCFVTSFIT ELVLMLLFLT ILAFCSAVLL IIYRIGQEFE RSKVPDDRLY EELHVYSPIY SALEDTREAS AP VVS

UniProtKB: High affinity immunoglobulin epsilon receptor subunit beta

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Macromolecule #3: High affinity immunoglobulin epsilon receptor subunit gamma

MacromoleculeName: High affinity immunoglobulin epsilon receptor subunit gamma
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 13.459315 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MIPAVILFLL LLVEEAAALG EPQLCYILDA ILFLYGIVLT LLYCRLKIQV RKADIASREK SDAVYTGLNT RNQETYETLK HEKPPQGSG WSHPQFEKGS GDYKDDDDKG SGWSHPQFEK

UniProtKB: High affinity immunoglobulin epsilon receptor subunit gamma

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Macromolecule #4: Immunoglobulin heavy constant epsilon

MacromoleculeName: Immunoglobulin heavy constant epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 41.815438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSVPTQVLGL LLLWLTDARC DIARPVNITK PTVDLLHSSC DPNAFHSTIQ LYCFVYGHIQ NDVSIHWLMD DRKIYETHAQ NVLIKEEGK LASTYSRLNI TQQQWMSEST FTCKVTSQGE NYWAHTRRCS DDEPRGVITY LIPPSPLDLY ENGTPKLTCL V LDLESEEN ...String:
MSVPTQVLGL LLLWLTDARC DIARPVNITK PTVDLLHSSC DPNAFHSTIQ LYCFVYGHIQ NDVSIHWLMD DRKIYETHAQ NVLIKEEGK LASTYSRLNI TQQQWMSEST FTCKVTSQGE NYWAHTRRCS DDEPRGVITY LIPPSPLDLY ENGTPKLTCL V LDLESEEN ITVTWVRERK KSIGSASQRS TKHHNATTSI TSILPVDAKD WIEGEGYQCR VDHPHFPKPI VRSITKAPGK RS APEVYVF LPPEEEEKDK RTLTCLIQNF FPEDISVQWL QDSKLIPKSQ HSTTTPLKYN GSNQRFFIFS RLEVTKALWT QTK QFTCRV IHEALREPRK LERTISKSLG NTSLRPSQAS MHHHHHH

UniProtKB: Immunoglobulin heavy constant epsilon

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #8: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 690272
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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