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- EMDB-36941: Mouse Fc epsilon RI in complex with mIgE Fc -

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Basic information

Entry
Database: EMDB / ID: EMD-36941
TitleMouse Fc epsilon RI in complex with mIgE Fc
Map data
Sample
  • Complex: Mouse Fc epsilon RI in complex with mIgE Fc
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit alpha
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit gamma
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit beta
    • Protein or peptide: IgE Fc
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIgE / high-affinity IgE receptor / allergy / IMMUNE SYSTEM
Function / homology
Function and homology information


Platelet Adhesion to exposed collagen / serotonin secretion / Fc epsilon receptor (FCERI) signaling / Dectin-2 family / IgE receptor activity / Fc-epsilon receptor I complex / Role of LAT2/NTAL/LAB on calcium mobilization / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / negative regulation of mast cell apoptotic process ...Platelet Adhesion to exposed collagen / serotonin secretion / Fc epsilon receptor (FCERI) signaling / Dectin-2 family / IgE receptor activity / Fc-epsilon receptor I complex / Role of LAT2/NTAL/LAB on calcium mobilization / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / negative regulation of mast cell apoptotic process / GPVI-mediated activation cascade / FCERI mediated MAPK activation / mast cell activation / mast cell apoptotic process / FCERI mediated Ca+2 mobilization / FCERI mediated NF-kB activation / positive regulation of interleukin-3 production / Cell surface interactions at the vascular wall / serotonin secretion by platelet / positive regulation of mast cell cytokine production / neutrophil activation involved in immune response / positive regulation of mast cell degranulation / positive regulation of type III hypersensitivity / Fc-gamma receptor signaling pathway / regulation of platelet activation / positive regulation of type IIa hypersensitivity / IgE binding / leukotriene biosynthetic process / positive regulation of type I hypersensitivity / positive regulation of protein localization to cell surface / interleukin-3-mediated signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / IgG binding / phagocytosis, engulfment / mast cell degranulation / positive regulation of interleukin-4 production / antigen processing and presentation of exogenous peptide antigen via MHC class I / immunoglobulin mediated immune response / positive regulation of interleukin-10 production / cellular response to low-density lipoprotein particle stimulus / regulation of immune response / positive regulation of phagocytosis / neutrophil chemotaxis / Neutrophil degranulation / positive regulation of calcium-mediated signaling / osteoclast differentiation / integrin-mediated signaling pathway / protein localization to plasma membrane / establishment of localization in cell / calcium-mediated signaling / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / receptor internalization / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell surface receptor signaling pathway / defense response to bacterium / immune response / membrane raft / external side of plasma membrane / innate immune response / cell surface / signal transduction / metal ion binding / identical protein binding / plasma membrane
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 subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
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 speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsZhang Z / Yui M / Ohto U / Shimizu T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Signal / Year: 2024
Title: Architecture of the high-affinity immunoglobulin E receptor.
Authors: Zhikuan Zhang / Moeko Yui / Umeharu Ohto / Toshiyuki Shimizu /
Abstract: The high-affinity immunoglobulin E (IgE) receptor (FcεRI) drives type I hypersensitivity in response to allergen-specific IgE. FcεRI is a multimeric complex typically composed of one α, one β, ...The high-affinity immunoglobulin E (IgE) receptor (FcεRI) drives type I hypersensitivity in response to allergen-specific IgE. FcεRI is a multimeric complex typically composed of one α, one β, and two disulfide-linked γ subunits. The α subunit binds to the fragment crystallizable (Fc) region of IgE (Fcε), whereas the β and γ subunits mediate signaling through their intracellular immunoreceptor tyrosine-based activation motifs (ITAMs). Here, we report cryo-electron microscopy (cryo-EM) structures of the apo state of FcεRI and of FcεRI bound to Fcε. At the transmembrane domain (TMD), the α and γ subunits associate to form a tightly packed, three-helix bundle (αγ bundle) with pseudo-threefold symmetry through extensive hydrophobic and polar interactions. The αγ bundle further assembles with the β subunit to complete the TMD, from which multiple ITAMs might extend into the cytoplasm for downstream signaling. The apo mouse FcεRI essentially forms an identical structure to that of the Fcε-bound sensitized form, suggesting that the binding of Fcε to FcεRI does not alter the overall conformation of the receptor. Furthermore, the juxtamembrane interaction between the extracellular domains (ECDs) of mouse FcεRIα and FcεRIβ is not observed between their human counterparts, which implies potential species-specific differences in receptor stability and activation. Our findings provide a framework for understanding the general structural principles underlying Fc receptor assembly, the signaling mechanism underlying type I hypersensitivity, and the design of efficient antiallergic therapeutics.
History
DepositionJul 27, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36941.png

Downloads & links

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Map

FileDownload / File: emd_36941.map.gz / Format: CCP4 / Size: 52.7 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.)
1.25 Å/pix.
x 240 pix.
= 298.8 Å		1.25 Å/pix.
x 240 pix.
= 298.8 Å		1.25 Å/pix.
x 240 pix.
= 298.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-4.9883003 - 6.421056
Average (Standard dev.)0.00072881597 (±0.124121085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_36941_additional_1.map
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Half map: #2

Fileemd_36941_half_map_1.map
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Half map: #1

Fileemd_36941_half_map_2.map
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Sample components

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Entire : Mouse Fc epsilon RI in complex with mIgE Fc

EntireName: Mouse Fc epsilon RI in complex with mIgE Fc
Components
  • Complex: Mouse Fc epsilon RI in complex with mIgE Fc
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit alpha
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit gamma
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit beta
    • Protein or peptide: IgE Fc
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Mouse Fc epsilon RI in complex with mIgE Fc

SupramoleculeName: Mouse Fc epsilon RI in complex with mIgE Fc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)

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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: Mus musculus (house mouse)
Molecular weightTheoretical: 31.646197 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVTGRSAQLC LALLFMSLDV ILTATEKSVL TLDPPWIRIF TGEKVTLSCY GNNHLQMNST TKWIHNGTVS EVNSSHLVIV SATVQDSGK YICQKQGLFK SKPVYLNVTQ DWLLLQTSAD MVLVHGSFDI RCHGWKNWNV RKVIYYRNDH AFNYSYESPV S IREATLND ...String:
MVTGRSAQLC LALLFMSLDV ILTATEKSVL TLDPPWIRIF TGEKVTLSCY GNNHLQMNST TKWIHNGTVS EVNSSHLVIV SATVQDSGK YICQKQGLFK SKPVYLNVTQ DWLLLQTSAD MVLVHGSFDI RCHGWKNWNV RKVIYYRNDH AFNYSYESPV S IREATLND SGTYHCKGYL RQVKYESDKF RIAVVKAYKC KYYWLQLIFP LLVAILFAVD TGLLLSTEEQ FKSVLEIQKT GK YKKVETE LLTENLYFQG DYKDDDDKHH HHHHHH

UniProtKB: High affinity immunoglobulin epsilon receptor subunit alpha

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Macromolecule #2: High affinity immunoglobulin epsilon receptor subunit gamma

MacromoleculeName: High affinity immunoglobulin epsilon receptor subunit gamma
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.890856 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MISAVILFLL LLVEQAAALG EPQLCYILDA VLFLYGIVLT LLYCRLKIQV RKAAIASREK ADAVYTGLNT RSQETYETLK HEKPPQWSH PQFEKEQKLI SEEDL

UniProtKB: High affinity immunoglobulin epsilon receptor subunit gamma

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Macromolecule #3: High affinity immunoglobulin epsilon receptor subunit beta

MacromoleculeName: High affinity immunoglobulin epsilon receptor subunit beta
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.166141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDTENRSRAD LALPNPQESS SAPDIELLEA SPAKAAPPKQ TWRTFLKKEL EFLGATQILV GLICLCFGTI VCSVLYVSDF DEEVLLLYK LGYPFWGAVL FVLSGFLSII SERKNTLYLV RGSLGANIVS SIAAGTGIAM LILNLTNNFA YMNNCKNVTE D DGCFVASF ...String:
MDTENRSRAD LALPNPQESS SAPDIELLEA SPAKAAPPKQ TWRTFLKKEL EFLGATQILV GLICLCFGTI VCSVLYVSDF DEEVLLLYK LGYPFWGAVL FVLSGFLSII SERKNTLYLV RGSLGANIVS SIAAGTGIAM LILNLTNNFA YMNNCKNVTE D DGCFVASF TTELVLMMLF LTILAFCSAV LFTIYRIGQE LESKKVPDDR LYEELNVYSP IYSELEDKGE TSSPVDSEQK LI SEEDL

UniProtKB: High affinity immunoglobulin epsilon receptor subunit beta

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Macromolecule #4: IgE Fc

MacromoleculeName: IgE Fc / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 40.369723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METGLRWLLL VAVLKGVQCV RPVNITDPTL ELLHSSCDPN AFHSTIQLYC FIYGHILNDV SVSWLMDDRE ITDTLAQTVL IKEEGKLAS TCSKLNITEQ QWMSESTFTC KVTSQGVDYL AHTRRCPDHE PRGVITYLIP PSPLDLYQNG APKLTCLVVD L ESEKNVNV ...String:
METGLRWLLL VAVLKGVQCV RPVNITDPTL ELLHSSCDPN AFHSTIQLYC FIYGHILNDV SVSWLMDDRE ITDTLAQTVL IKEEGKLAS TCSKLNITEQ QWMSESTFTC KVTSQGVDYL AHTRRCPDHE PRGVITYLIP PSPLDLYQNG APKLTCLVVD L ESEKNVNV TWNQEKKTSV SASQWYTKHH NNATTSITSI LPVVAKDWIE GYGYQCIVDH PDFPKPIVRS ITKTPGQRSA PE VYVFPPP EEESEDKRTL TCLIQNFFPE DISVQWLGDG KLISNSQHST TTPLKSNGSN QGFFIFSRLE VAKTLWTQRK QFT CQVIHE ALQKPRKLEK TISTSLGNTS LRPSHHHHHH

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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: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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: 7.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91911
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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