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- PDB-8zgs: Structure of the ige-fc bound to its high affinity receptor fc(ep... -

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Entry
Database: PDB / ID: 8zgs
TitleStructure of the ige-fc bound to its high affinity receptor fc(epsilon)ri state2
Components
  • (High affinity immunoglobulin epsilon receptor subunit ...) x 3
  • Immunoglobulin heavy constant epsilon
KeywordsMEMBRANE PROTEIN / Complex
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 / IgE receptor activity / Fc-epsilon receptor I complex / Cell surface interactions at the vascular wall ...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 / IgE receptor activity / Fc-epsilon receptor I complex / Cell surface interactions at the vascular wall / FCERI mediated Ca+2 mobilization / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / negative regulation of mast cell apoptotic process / high-affinity IgE receptor activity / IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / mast cell activation / Fc-gamma receptor III complex / FCERI mediated MAPK activation / positive regulation of interleukin-3 production / eosinophil degranulation / serotonin secretion by platelet / humoral immune response mediated by circulating immunoglobulin / neutrophil activation involved in immune response / positive regulation of mast cell degranulation / positive regulation of mast cell cytokine production / positive regulation of type III hypersensitivity / Fc-gamma receptor signaling pathway / regulation of platelet activation / positive regulation of type IIa hypersensitivity / macrophage activation / histamine secretion by mast cell / positive regulation of type I hypersensitivity / IgE binding / leukotriene biosynthetic process / interleukin-3-mediated signaling pathway / positive regulation of protein localization to cell surface / antibody-dependent cellular cytotoxicity / regulation of release of sequestered calcium ion into cytosol / positive regulation of granulocyte macrophage colony-stimulating factor production / type 2 immune response / IgG binding / immunoglobulin complex, circulating / Neutrophil degranulation / phagocytosis, engulfment / immunoglobulin receptor binding / mast cell degranulation / antigen processing and presentation of exogenous peptide antigen via MHC class I / Fc-epsilon receptor signaling pathway / positive regulation of interleukin-4 production / immunoglobulin mediated immune response / B cell proliferation / macrophage differentiation / positive regulation of interleukin-10 production / regulation of immune response / cellular response to low-density lipoprotein particle stimulus / antigen binding / neutrophil chemotaxis / positive regulation of calcium-mediated signaling / osteoclast differentiation / positive regulation of phagocytosis / SH2 domain binding / establishment of localization in cell / B cell differentiation / B cell receptor signaling pathway / integrin-mediated signaling pathway / protein localization to plasma membrane / phosphoprotein binding / peptide antigen assembly with MHC class II protein complex / receptor internalization / MHC class II protein complex / positive regulation of interleukin-6 production / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / positive regulation of T cell activation / positive regulation of tumor necrosis factor production / 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 / innate immune response / lysosomal membrane / protein kinase binding / cell surface / signal transduction / protein homodimerization activity / : / extracellular region / 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 / Immunoglobulin domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
CHOLESTEROL HEMISUCCINATE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsDu, S. / Deng, M.J. / Xiao, J.Y.
Funding support1items
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
DepositionMay 9, 2024Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: High affinity immunoglobulin epsilon receptor subunit alpha
B: High affinity immunoglobulin epsilon receptor subunit beta
C: High affinity immunoglobulin epsilon receptor subunit gamma
E: Immunoglobulin heavy constant epsilon
F: Immunoglobulin heavy constant epsilon
G: High affinity immunoglobulin epsilon receptor subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,62915
Polymers160,4396
Non-polymers3,1909
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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High affinity immunoglobulin epsilon receptor subunit ... , 3 types, 4 molecules ABCG

#1: Protein High affinity immunoglobulin epsilon receptor subunit alpha / Fc-epsilon RI-alpha / FcERI / IgE Fc receptor subunit alpha


Mass: 27830.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P12371
#2: Protein High affinity immunoglobulin epsilon receptor subunit beta / FcERI / Fc epsilon receptor I beta-chain / IgE Fc receptor subunit beta


Mass: 26747.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P13386
#3: Protein High affinity immunoglobulin epsilon receptor subunit gamma / Fc receptor gamma-chain / FcRgamma / Fc-epsilon RI-gamma / IgE Fc receptor subunit gamma / FceRI gamma


Mass: 9774.509 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P20411

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Protein / Non-polymers , 2 types, 3 molecules EF

#4: Protein Immunoglobulin heavy constant epsilon / Ig epsilon chain C region


Mass: 43155.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: IGHE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01855
#8: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION

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Sugars , 3 types, 8 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ige-fc bound to its high affinity receptor fc(epsilon)ri
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280787 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0069121
ELECTRON MICROSCOPYf_angle_d0.58312382
ELECTRON MICROSCOPYf_dihedral_angle_d4.9531263
ELECTRON MICROSCOPYf_chiral_restr0.0421453
ELECTRON MICROSCOPYf_plane_restr0.0061519

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