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

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Basic information

Entry
Database: PDB / ID: 8zgt
TitleStructure of the ige-fc bound to its high affinity receptor fc(epsilon)ri state3
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 / Cell surface interactions at the vascular wall / IgE receptor activity / Fc-epsilon receptor I complex ...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 / Cell surface interactions at the vascular wall / IgE receptor activity / Fc-epsilon receptor I complex / FCERI mediated Ca+2 mobilization / negative regulation of mast cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / high-affinity IgE receptor activity / IgE B cell receptor complex / type I hypersensitivity / mast cell apoptotic process / mast cell activation / Fc-gamma receptor III complex / FCERI mediated MAPK activation / positive regulation of interleukin-3 production / eosinophil degranulation / serotonin secretion by platelet / positive regulation of mast cell cytokine production / neutrophil activation involved in immune response / positive regulation of type III hypersensitivity / positive regulation of mast cell degranulation / Fc-gamma receptor signaling pathway / regulation of platelet activation / positive regulation of type IIa hypersensitivity / IgE binding / leukotriene biosynthetic process / positive regulation of protein localization to cell surface / regulation of release of sequestered calcium ion into cytosol / positive regulation of type I hypersensitivity / interleukin-3-mediated signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / type 2 immune response / IgG binding / Neutrophil degranulation / immunoglobulin receptor binding / phagocytosis, engulfment / mast cell degranulation / positive regulation of interleukin-4 production / antigen processing and presentation of exogenous peptide antigen via MHC class I / Fc-epsilon receptor signaling pathway / 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 / B cell differentiation / SH2 domain binding / osteoclast differentiation / positive regulation of calcium-mediated signaling / protein localization to plasma membrane / integrin-mediated signaling pathway / establishment of localization in cell / B cell receptor signaling pathway / phosphoprotein binding / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / calcium-mediated signaling / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / receptor internalization / positive regulation of interleukin-6 production / 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 / lysosomal membrane / innate immune response / protein kinase binding / cell surface / signal transduction / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytoplasm
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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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: 2.96 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
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.3Oct 16, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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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 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}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

Component
IDNameTypeEntity IDParent-IDSource
1ige-fc bound to its high affinity receptor fc(epsilon)riCOMPLEX#4, #1-#30MULTIPLE SOURCES
2High affinity immunoglobulin epsilon receptorCOMPLEX#1-#31NATURAL
3IgECOMPLEX#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Rattus norvegicus (Norway rat)10116
32Rattus norvegicus (Norway rat)10116
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 350802 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049122
ELECTRON MICROSCOPYf_angle_d0.75312385
ELECTRON MICROSCOPYf_dihedral_angle_d5.7761264
ELECTRON MICROSCOPYf_chiral_restr0.051453
ELECTRON MICROSCOPYf_plane_restr0.0061520

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