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- EMDB-39614: structure of Ige receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-39614
Titlestructure of Ige receptor
Map data
Sample
  • Complex: Structure of ige receptor
    • 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
  • Ligand: CHOLESTEROL
Keywordsimmunology / Ige receptor / allergy / MEMBRANE PROTEIN
Function / homology
Function and homology information


IgE receptor activity / Fc-epsilon receptor I complex / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / high-affinity IgE receptor activity / type I hypersensitivity / Fc-gamma receptor III complex / eosinophil degranulation / neutrophil activation involved in immune response / Fc-gamma receptor signaling pathway ...IgE receptor activity / Fc-epsilon receptor I complex / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / high-affinity IgE receptor activity / type I hypersensitivity / Fc-gamma receptor III complex / eosinophil degranulation / neutrophil activation involved in immune response / Fc-gamma receptor signaling pathway / regulation of platelet activation / Platelet Adhesion to exposed collagen / IgE binding / type 2 immune response / interleukin-3-mediated signaling pathway / Fc epsilon receptor (FCERI) signaling / IgG binding / mast cell degranulation / positive regulation of interleukin-4 production / Dectin-2 family / Fc-epsilon receptor signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class I / tertiary granule membrane / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of phagocytosis / GPVI-mediated activation cascade / neutrophil chemotaxis / FCERI mediated Ca+2 mobilization / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / receptor internalization / FCERI mediated NF-kB activation / antigen processing and presentation of exogenous peptide antigen via MHC class II / cell surface receptor signaling pathway / defense response to bacterium / immune response / external side of plasma membrane / innate immune response / Neutrophil degranulation / cell surface / protein homodimerization activity / 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 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 / High affinity immunoglobulin epsilon receptor subunit gamma / High affinity immunoglobulin epsilon receptor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsChen MY / Su Q / Shi YG
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)81920108015 China
CitationJournal: Nature / Year: 2024
Title: Molecular mechanism of IgE-mediated FcεRI activation.
Authors: Mengying Chen / Qiang Su / Yigong Shi /
Abstract: Allergic diseases, affecting over a quarter of individuals in industrialized countries, have become significant public health concerns. The high-affinity Fc receptor for IgE (FcεRI), mainly present ...Allergic diseases, affecting over a quarter of individuals in industrialized countries, have become significant public health concerns. The high-affinity Fc receptor for IgE (FcεRI), mainly present on mast cells and basophils, plays a crucial role in allergic diseases. Monomeric IgE binding to FcεRI regulates mast cell survival, differentiation, and maturation. However, the underlying molecular mechanism remains unclear. Here we demonstrate that, prior to IgE binding, FcεRI mostly exists as a homo-dimer on human mast cell membrane. The structure of human FcεRI confirms the dimeric organization, with each promoter comprising one α subunit, one β subunit, and two γ subunits. The transmembrane helices of the α subunits form a layered arrangement with those of the γ and β subunits. The dimeric interface is mediated by a four-helix bundle of the α and γ subunits at the intracellular juxtamembrane region. Cholesterol-like molecules embedded within the transmembrane domain may stabilize the dimeric assembly. Upon IgE binding, the dimeric FcεRI dissociates into two protomers, each binding to an IgE molecule. Importantly, this process elicits transcriptional activation of Egr1/3 and Ccl2 in rat basophils, which can be attenuated by inhibiting the FcεRI dimer-to-monomer transition. Collectively, our study unveils the mechanism of antigen-independent, IgE-mediated FcεRI activation.
History
DepositionMar 29, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39614.png

Downloads & links

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Map

FileDownload / File: emd_39614.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 128 pix.
= 208.704 Å		1.63 Å/pix.
x 128 pix.
= 208.704 Å		1.63 Å/pix.
x 128 pix.
= 208.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6305 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.03
Minimum - Maximum-7.628539 - 13.246256000000001
Average (Standard dev.)0.008089415 (±0.20151392)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 208.70401 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39614_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_39614_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Structure of ige receptor

EntireName: Structure of ige receptor
Components
  • Complex: Structure of ige receptor
    • 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
  • Ligand: CHOLESTEROL

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Supramolecule #1: Structure of ige receptor

SupramoleculeName: Structure of ige receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.375302 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
KYWLQFFIPL LVVILFAVDT GLFISTQQQV TFLLKIK

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.309385 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TWLTVLKKEQ EFLGVTQILT AMICLCFGTV VCSVLDISHI EGDIFSSFKA GYPFWGAIFF SISGMLSIIS ERRNATYLVR GSLGANTAS SIAGGTGITI LIINLKKSLA YIHIHSCQKF FETKCFMASF STEIVVMMLF LTILGLGSAV SLTICGAGEE L

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: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.552554 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PQLCYILDAI LFLYGIVLTL LYCRLKIQVR KAAITSYEK

UniProtKB: High affinity immunoglobulin epsilon receptor subunit gamma

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.2 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170032
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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