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- PDB-21nz: Cryo-EM structure of the rat IgE-Fc in complex with FcgammaRIV -

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Basic information

Entry
Database: PDB / ID: 21nz
TitleCryo-EM structure of the rat IgE-Fc in complex with FcgammaRIV
Components
  • Immunoglobulin heavy constant epsilon
  • Low affinity immunoglobulin gamma Fc region receptor III-A
KeywordsIMMUNE SYSTEM / antibody
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / IgE receptor activity / dendritic cell antigen processing and presentation / low-affinity IgG receptor activity / natural killer cell degranulation / IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / IgG receptor activity / B cell antigen processing and presentation ...Post-translational modification: synthesis of GPI-anchored proteins / IgE receptor activity / dendritic cell antigen processing and presentation / low-affinity IgG receptor activity / natural killer cell degranulation / IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / IgG receptor activity / B cell antigen processing and presentation / positive regulation of mast cell degranulation / type I hypersensitivity / immune receptor activity / Fc receptor-mediated immune complex endocytosis / Fc-gamma receptor III complex / positive regulation of natural killer cell proliferation / eosinophil degranulation / Fc-gamma receptor signaling pathway / neutrophil activation / macrophage activation / IgE binding / positive regulation of bone resorption / antibody-dependent cellular cytotoxicity / natural killer cell activation / B cell proliferation / type 2 immune response / IgG binding / natural killer cell mediated cytotoxicity / Neutrophil degranulation / immunoglobulin receptor binding / macrophage differentiation / B cell receptor signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / calcium-mediated signaling / mast cell degranulation / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / 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 / cellular response to lipopolysaccharide / cell surface receptor signaling pathway / external side of plasma membrane / lysosomal membrane / cell surface / : / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
beta-D-mannopyranose / Immunoglobulin heavy constant epsilon / Low affinity immunoglobulin gamma Fc region receptor III-A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsXu, S.R. / Du, S. / Xiao, J.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the rat IgE-Fc in complex with FcgammaRIV
Authors: Xu, S.R. / Du, S. / Xiao, J.Y.
History
DepositionDec 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low affinity immunoglobulin gamma Fc region receptor III-A
B: Immunoglobulin heavy constant epsilon
C: Immunoglobulin heavy constant epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,11713
Polymers111,0133
Non-polymers3,10510
Water00
1


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

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Low affinity immunoglobulin gamma Fc region receptor III-A / IgG Fc receptor III-A / CD16-2 / FcgammaRIV


Mass: 27381.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fcgr3a, Fcgr4 / Production host: Homo sapiens (human) / References: UniProt: Q6XPU4
#2: Protein Immunoglobulin heavy constant epsilon / Ig epsilon chain C region


Mass: 41815.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: IGHE / Production host: Homo sapiens (human) / References: UniProt: P01855

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Sugars , 4 types, 10 molecules

#3: 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
#4: 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
#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.: 6 / 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
#6: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG 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: Rat Fc epsilon in complex with FcgammaRIV / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1138601 / Symmetry type: POINT
RefinementHighest resolution: 2.98 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026835
ELECTRON MICROSCOPYf_angle_d0.5029277
ELECTRON MICROSCOPYf_dihedral_angle_d4.93965
ELECTRON MICROSCOPYf_chiral_restr0.0441068
ELECTRON MICROSCOPYf_plane_restr0.0041166

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