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- EMDB-67856: Cryo-EM structure of the rat IgE-Fc in complex with FcgammaRIIB -

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Basic information

Entry
Database: EMDB / ID: EMD-67856
TitleCryo-EM structure of the rat IgE-Fc in complex with FcgammaRIIB
Map data
Sample
  • Complex: Rat Fc epsilon in complex with FcgammaRIIB
    • Protein or peptide: Low affinity immunoglobulin gamma Fc region receptor II
    • Protein or peptide: Immunoglobulin heavy constant epsilon
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose
Keywordsantibody / IMMUNE SYSTEM
Function / homology
Function and homology information


IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / B cell antigen processing and presentation / positive regulation of mast cell degranulation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / macrophage activation / antibody-dependent cellular cytotoxicity ...IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / B cell antigen processing and presentation / positive regulation of mast cell degranulation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / macrophage activation / antibody-dependent cellular cytotoxicity / B cell proliferation / type 2 immune response / immunoglobulin receptor binding / macrophage differentiation / B cell receptor signaling pathway / 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 / MHC class II protein complex binding / late endosome membrane / lysosomal membrane / : / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / : / 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 / Immunoglobulin domain / : / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsXu SR / Du S / Xiao JY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the rat IgE-Fc in complex with FcgammaRIIB
Authors: Xu SR / Du S / Xiao JY
History
DepositionDec 21, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67856.png

Downloads & links

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Map

FileDownload / File: emd_67856.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 280 pix.
= 266. Å		0.95 Å/pix.
x 280 pix.
= 266. Å		0.95 Å/pix.
x 280 pix.
= 266. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.195
Minimum - Maximum-1.3572645 - 1.8341423
Average (Standard dev.)0.000199493 (±0.032444056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 266.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67856_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67856_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67856_half_map_2.map
Projections & Slices
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Sample components

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Entire : Rat Fc epsilon in complex with FcgammaRIIB

EntireName: Rat Fc epsilon in complex with FcgammaRIIB
Components
  • Complex: Rat Fc epsilon in complex with FcgammaRIIB
    • Protein or peptide: Low affinity immunoglobulin gamma Fc region receptor II
    • Protein or peptide: Immunoglobulin heavy constant epsilon
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose

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Supramolecule #1: Rat Fc epsilon in complex with FcgammaRIIB

SupramoleculeName: Rat Fc epsilon in complex with FcgammaRIIB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Low affinity immunoglobulin gamma Fc region receptor II

MacromoleculeName: Low affinity immunoglobulin gamma Fc region receptor II
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 28.627162 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSNRTVVHV LSRTLYHMLL WTAVLNLVAE SHAGLPKAVV KLEPPWIQVL KEDTVTLMCE GTHNTKNCST QWFHNGSSIW HQAQANYTF KATVNDSGEY RCRMEETGIS EPIHLGVISD WLLLQTSQLV FEEGETITLR CHSWKNKQLT KVLLFQNGKP V RYYHQSSN ...String:
MDSNRTVVHV LSRTLYHMLL WTAVLNLVAE SHAGLPKAVV KLEPPWIQVL KEDTVTLMCE GTHNTKNCST QWFHNGSSIW HQAQANYTF KATVNDSGEY RCRMEETGIS EPIHLGVISD WLLLQTSQLV FEEGETITLR CHSWKNKQLT KVLLFQNGKP V RYYHQSSN FSIPKANHSH SGNYYCKAYL GRTMHVSKPV TITVQEPKSS SSLPGGSHHH HHHHHGSSAW SHPQFEKGGG SG GGSGGSA WSHPQFEK

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Macromolecule #2: Immunoglobulin heavy constant epsilon

MacromoleculeName: Immunoglobulin heavy constant epsilon / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 41.815438 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 MHHHHHH

UniProtKB: Immunoglobulin heavy constant epsilon

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
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: DARK FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1138601
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1138601
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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