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- EMDB-39627: The structure of IgE receptor binding to IgE -

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Basic information

Entry
Database: EMDB / ID: EMD-39627
TitleThe structure of IgE receptor binding to IgE
Map data
Sample
  • Complex: The structure of IgE receptor binding to IgE
    • 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
    • Protein or peptide: Immunoglobulin kappa constant
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsimmunology / Ige receptor / allergy / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
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 / interleukin-3-mediated signaling pathway / Fc epsilon receptor (FCERI) signaling / type 2 immune response / IgG binding / mast cell degranulation / Dectin-2 family / positive regulation of interleukin-4 production / antigen processing and presentation of exogenous peptide antigen via MHC class I / Fc-epsilon receptor signaling pathway / tertiary granule membrane / immunoglobulin mediated immune response / cellular response to low-density lipoprotein particle stimulus / ficolin-1-rich granule membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / receptor internalization / FCERI mediated NF-kB activation / 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: 3.14 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: 2025
Title: Molecular mechanism of IgE-mediated FcεRI activation.
Authors: Mengying Chen / Qiang Su / Yigong Shi /
Abstract: Allergic diseases affect more than a quarter of individuals in industrialized countries, and are a major public health concern. The high-affinity Fc receptor for immunoglobulin E (FcεRI), which is ...Allergic diseases affect more than a quarter of individuals in industrialized countries, and are a major public health concern. The high-affinity Fc receptor for immunoglobulin E (FcεRI), which is mainly present on mast cells and basophils, has a crucial role in allergic diseases. Monomeric immunoglobulin E (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 exists mostly as a homodimer on human mast cell membranes. 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 of which binds to an IgE molecule. This process elicits transcriptional activation of Egr1, Egr3 and Ccl2 in rat basophils, which can be attenuated by inhibiting the FcεRI dimer-to-monomer transition. Collectively, our study reveals the mechanism of antigen-independent, IgE-mediated FcεRI activation.
History
DepositionMar 30, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39627.png

Downloads & links

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Map

FileDownload / File: emd_39627.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.42
Minimum - Maximum-4.2344966 - 7.114267
Average (Standard dev.)0.0045281267 (±0.103603624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 260.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39627_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_39627_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : The structure of IgE receptor binding to IgE

EntireName: The structure of IgE receptor binding to IgE
Components
  • Complex: The structure of IgE receptor binding to IgE
    • 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
    • Protein or peptide: Immunoglobulin kappa constant
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: The structure of IgE receptor binding to IgE

SupramoleculeName: The structure of IgE receptor binding to IgE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#5, #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Immunoglobulin heavy constant epsilon

MacromoleculeName: Immunoglobulin heavy constant epsilon / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.525254 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEFGLSWLFL VAILKGVQCQ VQLVQSGAEV RNPGASVKVS CKASGYTFTS YAIHWVRQAP GHRLEWVGRI NTDNGNTKYS QKFHGRVAL SRDTSASTTY MDLSSLNSED TAVYYCARAF YYSSGVMFDS WGQGALVTVS SASTQSPSVF PLTRCCKNIP S NATSVTLG ...String:
MEFGLSWLFL VAILKGVQCQ VQLVQSGAEV RNPGASVKVS CKASGYTFTS YAIHWVRQAP GHRLEWVGRI NTDNGNTKYS QKFHGRVAL SRDTSASTTY MDLSSLNSED TAVYYCARAF YYSSGVMFDS WGQGALVTVS SASTQSPSVF PLTRCCKNIP S NATSVTLG CLATGYFPEP VMVTWDTGSL NGTTMTLPAT TLTLSGHYAT ISLLTVSGAW AKQMFTCRVA HTPSSTDWVD NK TFSVCSR DFTPPTVKIL QSSCDGGGHF PPTIQLLCLV SGYTPGTINI TWLEDGQVMD VDLSTASTTQ EGELASTQSE LTL SQKHWL SDRTYTCQVT YQGHTFEDST KKCADSNPRG VSAYLSRPSP FDLFIRKSPT ITCLVVDLAP SKGTVNLTWS RASG KPVNH STRKEEKQRN GTLTVTSTLP VGTRDWIEGE TYQCRVTHPH LPRALMRSTT KTSGPRAAPE VYAFATPEWP GSRDK RTLA CLIQNFMPED ISVQWLHNEV QLPDARHSTT QPRKTKGSGF FVFSRLEVTR AEWEQKDEFI CRAVHEAASP SQTVQR AVS VNPGKGGSHH HHHH

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Macromolecule #2: Immunoglobulin kappa constant

MacromoleculeName: Immunoglobulin kappa constant / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.441352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLSGA RCGGSMDYKD DDDKGSPGDE VDAGQSALTQ PPSVSGAPGQ RVSISCTGGS SNFGAGYDVH WYQQLPATA PKLLIYGNNN RPSGVPDRFS GSKSGTSASL AITGLQAEDE GDYFCQSFDT SLSGWIFGGG TKLTVLGQPK A APSVTLFP ...String:
MDMRVPAQLL GLLLLWLSGA RCGGSMDYKD DDDKGSPGDE VDAGQSALTQ PPSVSGAPGQ RVSISCTGGS SNFGAGYDVH WYQQLPATA PKLLIYGNNN RPSGVPDRFS GSKSGTSASL AITGLQAEDE GDYFCQSFDT SLSGWIFGGG TKLTVLGQPK A APSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV ETTTPSKQSN NKYAASSYLS LTPEQWKSHR SY SCQVTHE GSTVEKTVAP TECS

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Macromolecule #3: High affinity immunoglobulin epsilon receptor subunit alpha

MacromoleculeName: High affinity immunoglobulin epsilon receptor subunit alpha
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.892074 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLSGA RCVPQKPKVS LNPPWNRIFK GENVTLTCNG NNFFEVSSTK WFHNGSLSEE TNSSLNIVNA KFEDSGEYK CQHQQVNESE PVYLEVFSDW LLLQASAEVV MEGQPLFLRC HGWRNWDVYK VIYYKDGEAL KYWYENHNIS I TNATVEDS ...String:
MDMRVPAQLL GLLLLWLSGA RCVPQKPKVS LNPPWNRIFK GENVTLTCNG NNFFEVSSTK WFHNGSLSEE TNSSLNIVNA KFEDSGEYK CQHQQVNESE PVYLEVFSDW LLLQASAEVV MEGQPLFLRC HGWRNWDVYK VIYYKDGEAL KYWYENHNIS I TNATVEDS GTYYCTGKVW QLDYESEPLN ITVIKAPREK YWLQFFIPLL VVILFAVDTG LFISTQQQVT FLLKIKRTRK GF RLLNPHP KPNPKNNGGG SMDYKDDDDK

UniProtKB: High affinity immunoglobulin epsilon receptor subunit alpha

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Macromolecule #4: High affinity immunoglobulin epsilon receptor subunit beta

MacromoleculeName: High affinity immunoglobulin epsilon receptor subunit beta
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.289541 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGASSAWSHP QFEKGGGSGG GSGGSAWSHP QFEKGSAAAM DTESNRRANL ALPQEPSSVP AFEVLEISPQ EVSSGRLLKS ASSPPLHTW LTVLKKEQEF LGVTQILTAM ICLCFGTVVC SVLDISHIEG DIFSSFKAGY PFWGAIFFSI SGMLSIISER R NATYLVRG ...String:
MGASSAWSHP QFEKGGGSGG GSGGSAWSHP QFEKGSAAAM DTESNRRANL ALPQEPSSVP AFEVLEISPQ EVSSGRLLKS ASSPPLHTW LTVLKKEQEF LGVTQILTAM ICLCFGTVVC SVLDISHIEG DIFSSFKAGY PFWGAIFFSI SGMLSIISER R NATYLVRG SLGANTASSI AGGTGITILI INLKKSLAYI HIHSCQKFFE TKCFMASFST EIVVMMLFLT ILGLGSAVSL TI CGAGEEL KGNKVPEDRV YEELNIYSAT YSELEDPGEM SPPIDL

UniProtKB: High affinity immunoglobulin epsilon receptor subunit beta

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Macromolecule #5: High affinity immunoglobulin epsilon receptor subunit gamma

MacromoleculeName: High affinity immunoglobulin epsilon receptor subunit gamma
type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.676426 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MIPAVVLLLL LLVEQAAALG EPQLCYILDA ILFLYGIVLT LLYCRLKIQV RKAAITSYEK SDGVYTGLST RNQETYETLK HEKPPQ

UniProtKB: High affinity immunoglobulin epsilon receptor subunit gamma

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 9 / 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: 7.5
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: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 920752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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