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- EMDB-36939: Human Fc epsilon RI in complex with hIgE Fc (TMD disordered) -

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Basic information

Entry
Database: EMDB / ID: EMD-36939
TitleHuman Fc epsilon RI in complex with hIgE Fc (TMD disordered)
Map dataSharpened map
Sample
  • Complex: Human Fc epsilon RI in complex with hIgE Fc
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit alpha
    • 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


high-affinity IgE receptor activity / type I hypersensitivity / eosinophil degranulation / IgE binding / Fc epsilon receptor (FCERI) signaling / type 2 immune response / mast cell degranulation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization ...high-affinity IgE receptor activity / type I hypersensitivity / eosinophil degranulation / IgE binding / Fc epsilon receptor (FCERI) signaling / type 2 immune response / mast cell degranulation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 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) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36939.png

Downloads & links

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Map

FileDownload / File: emd_36939.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 180 pix.
= 249. Å		1.38 Å/pix.
x 180 pix.
= 249. Å		1.38 Å/pix.
x 180 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-2.3205538 - 3.122548
Average (Standard dev.)0.0024332164 (±0.055603247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_36939_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_36939_half_map_1.map
AnnotationHalf map 2
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_36939_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : Human Fc epsilon RI in complex with hIgE Fc

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

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Supramolecule #1: Human Fc epsilon RI in complex with hIgE Fc

SupramoleculeName: Human Fc epsilon RI in complex with hIgE Fc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 32.578768 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPAMESPTL LCVALLFFAP DGVLAVPQKP KVSLNPPWNR IFKGENVTLT CNGNNFFEVS STKWFHNGSL SEETNSSLNI VNAKFEDSG EYKCQHQQVN ESEPVYLEVF SDWLLLQASA EVVMEGQPLF LRCHGWRNWD VYKVIYYKDG EALKYWYENH N ISITNATV ...String:
MAPAMESPTL LCVALLFFAP DGVLAVPQKP KVSLNPPWNR IFKGENVTLT CNGNNFFEVS STKWFHNGSL SEETNSSLNI VNAKFEDSG EYKCQHQQVN ESEPVYLEVF SDWLLLQASA EVVMEGQPLF LRCHGWRNWD VYKVIYYKDG EALKYWYENH N ISITNATV EDSGTYYCTG KVWQLDYESE PLNITVIKAP REKYWLQFFI PLLVVILFAV DTGLFISTQQ QVTFLLKIKR TR KGFRLLN PHPKPNPKNN ENLYFQGDYK DDDDKHHHHH HHH

UniProtKB: High affinity immunoglobulin epsilon receptor subunit alpha

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Macromolecule #2: IgE Fc

MacromoleculeName: IgE Fc / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.236145 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METGLRWLLL VAVLKGVQCQ SVASRDFTPP TVKILQSSCD GGGHFPPTIQ LLCLVSGYTP GTIQITWLED GQVMDVDLST ASTTQEGEL ASTQSELTLS QKHWLSDRTY TCQVTYQGHT FEDSTKKCAD SNPRGVSAYL SRPSPFDLFI RKSPTITCLV V DLAPSKGT ...String:
METGLRWLLL VAVLKGVQCQ SVASRDFTPP TVKILQSSCD GGGHFPPTIQ LLCLVSGYTP GTIQITWLED GQVMDVDLST ASTTQEGEL ASTQSELTLS QKHWLSDRTY TCQVTYQGHT FEDSTKKCAD SNPRGVSAYL SRPSPFDLFI RKSPTITCLV V DLAPSKGT VQLTWSRASG KPVNHSTRKE EKQRNGTLTV TSTLPVGTRD WIEGETYQCR VTHPHLPRAL MRSTTKTSGP RA APEVYAF ATPEWPGSRD KRTLACLIQN FMPEDISVQW LHNEVQLPDA RHSTTQPRKT KGSGFFVFSR LEVTRAEWEQ KDE FICRAV HEAASPSQTV QRAVSVNPHH HHHHH

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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: 2 / 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: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 303726
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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