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

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Basic information

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 / 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
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: To Be Published
Title: Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri state2
Authors: Du, S. / Deng, M.J. / Xiao, J.Y.
History
DepositionMay 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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