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- EMDB-67855: Cryo-EM structure of mouse IgG2b-Fc in complex with FcgammaRIV -

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Basic information

Entry
Database: EMDB / ID: EMD-67855
TitleCryo-EM structure of mouse IgG2b-Fc in complex with FcgammaRIV
Map data
Sample
  • Complex: mouse Fc gamma 2b in complex with FcgammaRIV
    • Protein or peptide: Low affinity immunoglobulin gamma Fc region receptor III-A
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant gamma 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody / IMMUNE SYSTEM
Function / homology
Function and homology information


IgE receptor activity / Post-translational modification: synthesis of GPI-anchored proteins / dendritic cell antigen processing and presentation / low-affinity IgG receptor activity / GPI anchor binding / natural killer cell degranulation / Classical antibody-mediated complement activation / IgG receptor activity / FCGR activation / Role of phospholipids in phagocytosis ...IgE receptor activity / Post-translational modification: synthesis of GPI-anchored proteins / dendritic cell antigen processing and presentation / low-affinity IgG receptor activity / GPI anchor binding / natural killer cell degranulation / Classical antibody-mediated complement activation / IgG receptor activity / FCGR activation / Role of phospholipids in phagocytosis / immune receptor activity / Fc receptor-mediated immune complex endocytosis / Regulation of Complement cascade / positive regulation of type IIa hypersensitivity / Fc-gamma receptor III complex / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / Regulation of actin dynamics for phagocytic cup formation / neutrophil activation / IgE binding / positive regulation of type I hypersensitivity / IgG immunoglobulin complex / positive regulation of bone resorption / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG binding / phagocytosis, engulfment / immunoglobulin receptor binding / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / Neutrophil degranulation / positive regulation of phagocytosis / positive regulation of immune response / cellular response to lipopolysaccharide / antibacterial humoral response / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / : / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / 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 domain / 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
Low affinity immunoglobulin gamma Fc region receptor III-A / Immunoglobulin heavy constant gamma 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsXu SR / Du S / Xiao JY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of mouse IgG2b-Fc in complex with FcgammaRIV
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_67855.png

Downloads & links

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Map

FileDownload / File: emd_67855.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.193
Minimum - Maximum-2.058548 - 2.8710144
Average (Standard dev.)-0.00026655578 (±0.04372887)
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_67855_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67855_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67855_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : mouse Fc gamma 2b in complex with FcgammaRIV

EntireName: mouse Fc gamma 2b in complex with FcgammaRIV
Components
  • Complex: mouse Fc gamma 2b in complex with FcgammaRIV
    • Protein or peptide: Low affinity immunoglobulin gamma Fc region receptor III-A
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant gamma 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: mouse Fc gamma 2b in complex with FcgammaRIV

SupramoleculeName: mouse Fc gamma 2b in complex with FcgammaRIV / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Low affinity immunoglobulin gamma Fc region receptor III-A

MacromoleculeName: Low affinity immunoglobulin gamma Fc region receptor III-A
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.763025 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWQLLLPTAL VLTAFSGIQA GLQKAVVNLD PKWVRVLEED SVTLRCQGTF SPEDNSIKWF HNESLIPHQD ANYVIQSARV KDSGMYRCQ TALSTISDPV QLEVHMGWLL LQTTKWLFQE GDPIHLRCHS WQNRPVRKVT YLQNGKGKKY FHENSELLIP K ATHNDSGS ...String:
MWQLLLPTAL VLTAFSGIQA GLQKAVVNLD PKWVRVLEED SVTLRCQGTF SPEDNSIKWF HNESLIPHQD ANYVIQSARV KDSGMYRCQ TALSTISDPV QLEVHMGWLL LQTTKWLFQE GDPIHLRCHS WQNRPVRKVT YLQNGKGKKY FHENSELLIP K ATHNDSGS YFCRGLIGHN NKSSASFRIS LGDPGSPSMF PPWHQGGSHH HHHHHHSRVD YKDDDDK

UniProtKB: Low affinity immunoglobulin gamma Fc region receptor III-A

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Macromolecule #2: Isoform 2 of Immunoglobulin heavy constant gamma 2B

MacromoleculeName: Isoform 2 of Immunoglobulin heavy constant gamma 2B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.472717 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS ARIHEPSGPI STINPCPPCK ECHKCPAPNL EGGPSVFIFP PNIKDVLMIS LTPKVTCVVV DVSEDDPDV QISWFVNNVE VHTAQTQTHR EDYNSTIRVV STLPIQHQDW MSGKEFKCKV NNKDLPSPIE RTISKIKGLV R APQVYILP ...String:
MYRMQLLSCI ALSLALVTNS ARIHEPSGPI STINPCPPCK ECHKCPAPNL EGGPSVFIFP PNIKDVLMIS LTPKVTCVVV DVSEDDPDV QISWFVNNVE VHTAQTQTHR EDYNSTIRVV STLPIQHQDW MSGKEFKCKV NNKDLPSPIE RTISKIKGLV R APQVYILP PPAEQLSRKD VSLTCLVVGF NPGDISVEWT SNGHTEENYK DTAPVLDSDG SYFIYSKLNM KTSKWEKTDS FS CNVRHEG LKNYYLKKTI SRSPGK

UniProtKB: Immunoglobulin heavy constant gamma 2B

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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: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 680209
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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