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- PDB-8yrj: Mouse Fc epsilon RI -

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Basic information

Entry
Database: PDB / ID: 8yrj
TitleMouse Fc epsilon RI
Components
  • High affinity immunoglobulin epsilon receptor subunit alpha
  • High affinity immunoglobulin epsilon receptor subunit beta
  • High affinity immunoglobulin epsilon receptor subunit gamma
KeywordsIMMUNE SYSTEM / IgE / high-affinity IgE receptor / allergy
Function / homology
Function and homology information


Platelet Adhesion to exposed collagen / serotonin secretion / Fc epsilon receptor (FCERI) signaling / Dectin-2 family / IgE receptor activity / Fc-epsilon receptor I complex / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of mast cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response ...Platelet Adhesion to exposed collagen / serotonin secretion / Fc epsilon receptor (FCERI) signaling / Dectin-2 family / IgE receptor activity / Fc-epsilon receptor I complex / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of mast cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / GPVI-mediated activation cascade / FCERI mediated MAPK activation / mast cell apoptotic process / mast cell activation / FCERI mediated Ca+2 mobilization / FCERI mediated NF-kB activation / positive regulation of interleukin-3 production / Cell surface interactions at the vascular wall / 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 / positive regulation of type I hypersensitivity / interleukin-3-mediated signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / IgG binding / phagocytosis, engulfment / mast cell degranulation / positive regulation of interleukin-4 production / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / Neutrophil degranulation / osteoclast differentiation / positive regulation of calcium-mediated signaling / protein localization to plasma membrane / integrin-mediated signaling pathway / establishment of localization in cell / calcium-mediated signaling / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / receptor internalization / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell surface receptor signaling pathway / defense response to bacterium / immune response / membrane raft / external side of plasma membrane / innate immune response / cell surface / signal transduction / metal ion binding / 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 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 beta / High affinity immunoglobulin epsilon receptor subunit gamma
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsZhang, Z. / Yui, M. / Ohto, U. / Shimizu, T.
Funding support1items
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
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.3Jan 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _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
G: High affinity immunoglobulin epsilon receptor subunit gamma
H: High affinity immunoglobulin epsilon receptor subunit gamma
B: High affinity immunoglobulin epsilon receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4319
Polymers82,5944
Non-polymers1,8375
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 31646.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fcer1a, Fce1a / Production host: Homo sapiens (human) / References: UniProt: P20489
#2: 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: 11890.856 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fcer1g, Fce1g / Production host: Homo sapiens (human) / References: UniProt: P20491
#3: Protein High affinity immunoglobulin epsilon receptor subunit beta / FcERI / Fc epsilon receptor I beta-chain / IgE Fc receptor subunit beta / Membrane-spanning 4- ...FcERI / Fc epsilon receptor I beta-chain / IgE Fc receptor subunit beta / Membrane-spanning 4-domains subfamily A member 2


Mass: 27166.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ms4a2, Fce1b, Fcer1b, Ms4a1 / Production host: Homo sapiens (human) / References: UniProt: P20490
#4: 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
#5: 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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
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
Has ligand of interestN
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: Mouse Fc epsilon RI / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97368 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023823
ELECTRON MICROSCOPYf_angle_d0.415183
ELECTRON MICROSCOPYf_dihedral_angle_d7.23554
ELECTRON MICROSCOPYf_chiral_restr0.036638
ELECTRON MICROSCOPYf_plane_restr0.003615

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