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- EMDB-60089: Structure of the ige-fc bound to its high affinity receptor fc(ep... -

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Basic information

Entry
Database: EMDB / ID: EMD-60089
TitleStructure of the ige-fc bound to its high affinity receptor fc(epsilon)ri state2
Map data
Sample
  • Complex: ige-fc bound to its high affinity receptor fc(epsilon)ri
    • 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
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsComplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


Fc epsilon receptor (FCERI) signaling / IgE receptor activity / Fc-epsilon receptor I complex / Dectin-2 family / serotonin secretion / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated NF-kB activation / Platelet Adhesion to exposed collagen / GPVI-mediated activation cascade / Cell surface interactions at the vascular wall ...Fc epsilon receptor (FCERI) signaling / IgE receptor activity / Fc-epsilon receptor I complex / Dectin-2 family / serotonin secretion / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated NF-kB activation / Platelet Adhesion to exposed collagen / GPVI-mediated activation cascade / Cell surface interactions at the vascular wall / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / FCERI mediated Ca+2 mobilization / negative regulation of mast cell apoptotic process / high-affinity IgE receptor activity / IgE B cell receptor complex / type I hypersensitivity / Fc-gamma receptor III complex / mast cell apoptotic process / mast cell activation / FCERI mediated MAPK activation / serotonin secretion by platelet / positive regulation of interleukin-3 production / eosinophil degranulation / Fc-gamma receptor signaling pathway / neutrophil activation involved in immune response / positive regulation of mast cell cytokine production / regulation of platelet activation / positive regulation of type III hypersensitivity / positive regulation of mast cell degranulation / IgE binding / positive regulation of type IIa hypersensitivity / type 2 immune response / positive regulation of protein localization to cell surface / regulation of release of sequestered calcium ion into cytosol / protein kinase C-activating G protein-coupled receptor signaling pathway / leukotriene biosynthetic process / positive regulation of type I hypersensitivity / interleukin-3-mediated signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / IgG binding / Neutrophil degranulation / 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 / positive regulation of interleukin-10 production / cellular response to low-density lipoprotein particle stimulus / regulation of immune response / immunoglobulin mediated immune response / positive regulation of calcium-mediated signaling / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / SH2 domain binding / B cell differentiation / neutrophil chemotaxis / osteoclast differentiation / complement activation, classical pathway / establishment of localization in cell / protein localization to plasma membrane / integrin-mediated signaling pathway / calcium-mediated signaling / phosphoprotein binding / B cell receptor signaling pathway / receptor internalization / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / antibacterial humoral response / cell surface receptor signaling pathway / blood microparticle / endosome / defense response to bacterium / immune response / protein heterodimerization activity / lysosomal membrane / external side of plasma membrane / innate immune response / protein kinase binding / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
High affinity immunoglobulin epsilon receptor subunit gamma / CD20-like family / Membrane-spanning 4-domains subfamily A / 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 ...High affinity immunoglobulin epsilon receptor subunit gamma / CD20-like family / Membrane-spanning 4-domains subfamily A / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsDu S / Deng MJ / Xiao JY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri state2
Authors: Du S / Deng MJ / Xiao JY
History
DepositionMay 9, 2024-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_60089.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.510944 - 2.0768752
Average (Standard dev.)0.00017378925 (±0.033577166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ige-fc bound to its high affinity receptor fc(epsilon)ri

EntireName: ige-fc bound to its high affinity receptor fc(epsilon)ri
Components
  • Complex: ige-fc bound to its high affinity receptor fc(epsilon)ri
    • 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
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: ige-fc bound to its high affinity receptor fc(epsilon)ri

SupramoleculeName: ige-fc bound to its high affinity receptor fc(epsilon)ri
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Rattus norvegicus (Norway rat)

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 27.83016 KDa
SequenceString: MDTGGSARLC LALVLISLGV MLTATQKSVV SLDPPWIRIL TGDKVTLICN GNNSSQMNST KWIHNDSISN VKSSHWVIVS ATIQDSGKY ICQKQGFYKS KPVYLNVMQE WLLLQSSADV VLDNGSFDIR CRSWKKWKVH KVIYYKDDIA FKYSYDSNNI S IRKATFND ...String:
MDTGGSARLC LALVLISLGV MLTATQKSVV SLDPPWIRIL TGDKVTLICN GNNSSQMNST KWIHNDSISN VKSSHWVIVS ATIQDSGKY ICQKQGFYKS KPVYLNVMQE WLLLQSSADV VLDNGSFDIR CRSWKKWKVH KVIYYKDDIA FKYSYDSNNI S IRKATFND SGSYHCTGYL NKVECKSDKF SIAVVKDYTI EYRWLQLIFP SLAVILFAVD TGLWFSTHKQ FESILKIQKT GK GKKKG

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: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 26.747752 KDa
SequenceString: MDTENKSRAD LALPNPQESP SAPDIELLEA SPPAKALPEK PASPPPQQTW QSFLKKELEF LGVTQVLVGL ICLCFGTVVC STLQTSDFD DEVLLLYRAG YPFWGAVLFV LSGFLSIMSE RKNTLYLVRG SLGANIVSSI AAGLGIAILI LNLSNNSAYM N YCKDITED ...String:
MDTENKSRAD LALPNPQESP SAPDIELLEA SPPAKALPEK PASPPPQQTW QSFLKKELEF LGVTQVLVGL ICLCFGTVVC STLQTSDFD DEVLLLYRAG YPFWGAVLFV LSGFLSIMSE RKNTLYLVRG SLGANIVSSI AAGLGIAILI LNLSNNSAYM N YCKDITED DGCFVTSFIT ELVLMLLFLT ILAFCSAVLL IIYRIGQEFE RSKVPDDRLY EELHVYSPIY SALEDTREAS AP VVS

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 9.774509 KDa
SequenceString:
MIPAVILFLL LLVEEAAALG EPQLCYILDA ILFLYGIVLT LLYCRLKIQV RKADIASREK SDAVYTGLNT RNQETYETLK HEKPPQ

UniProtKB: High affinity immunoglobulin epsilon receptor subunit gamma

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Macromolecule #4: Immunoglobulin heavy constant epsilon

MacromoleculeName: Immunoglobulin heavy constant epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 43.155809 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSVPTQVLGL LLLWLTDARC DIARPVNITK PTVDLLHSSC DPNAFHSTIQ LYCFVYGHIQ NDVSIHWLMD DRKIYETHAQ NVLIKEEGK LASTYSRLNI TQQQWMSEST FTCKVTSQGE NYWAHTRRCS DDEPRGVITY LIPPSPLDLY ENGTPKLTCL V LDLESEEN ...String:
MSVPTQVLGL LLLWLTDARC DIARPVNITK PTVDLLHSSC DPNAFHSTIQ LYCFVYGHIQ NDVSIHWLMD DRKIYETHAQ NVLIKEEGK LASTYSRLNI TQQQWMSEST FTCKVTSQGE NYWAHTRRCS DDEPRGVITY LIPPSPLDLY ENGTPKLTCL V LDLESEEN ITVTWVRERK KSIGSASQRS TKHHNATTSI TSILPVDAKD WIEGEGYQCR VDHPHFPKPI VRSITKAPGK RS APEVYVF LPPEEEEKDK RTLTCLIQNF FPEDISVQWL QDSKLIPKSQ HSTTTPLKYN GSNQRFFIFS RLEVTKALWT QTK QFTCRV IHEALREPRK LERTISKSLG NTSLRPSQAS MHHHHHHSRV DYKDDDDK

UniProtKB: Immunoglobulin heavy constant epsilon

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #8: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 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: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280787
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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