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- EMDB-64375: Cryo-EM structure of the Xenopus IgX-Fc hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-64375
TitleCryo-EM structure of the Xenopus IgX-Fc hexamer
Map data
Sample
  • Complex: the hexamer of the Xenopus IgX-Fc
    • Protein or peptide: Uncharacterized LOC101027262 precursor
KeywordsComplex / polymeric antibody / IMMUNE SYSTEM
Function / homology
Function and homology information


immunoglobulin receptor binding / immunoglobulin complex, circulating / complement activation, classical pathway / antigen binding / antibacterial humoral response
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
Uncharacterized LOC101027262 precursor
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsJi C / Zhang R / Xiao J
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Sci Adv / Year: 2025
Title: IgX informs engineering strategies of IgM and IgG hexamers.
Authors: Ruixue Zhang / Chenggong Ji / Shuhan Li / Ningning Li / Ning Gao / Junyu Xiao /
Abstract: Polymeric immunoglobulins are essential components of the immune system in jawed vertebrates. While mammalian immunoglobulin M (IgM) typically forms a pentamer linked by the joining chain (J-chain), ...Polymeric immunoglobulins are essential components of the immune system in jawed vertebrates. While mammalian immunoglobulin M (IgM) typically forms a pentamer linked by the joining chain (J-chain), IgX can assemble into a J-chain-independent polymer. Here, we present the cryo-electron microscopy (cryo-EM) structure of IgX, revealing its hexameric configuration. By incorporating the IgX tailpiece into human IgM, we achieved efficient IgM hexamer formation. Truncating IgM's natural tailpiece to a range of 11 to 16 residues also substantially enhanced hexamerization efficiency. Furthermore, introducing a shortened IgM tailpiece to IgG resulted in effective IgG hexamer formation. We further show that the engineered IgM and IgG hexamers targeting CD20 demonstrated robust complement-dependent cytotoxicity (CDC) against several B lymphoma cells. In addition, the IgG-Fc hexamer functioned as a decoy, attenuating CDC in cell cultures. These findings deepen our understanding of polymeric immunoglobulin evolution and introduce innovative strategies for the development of IgM- and IgG-based biologics.
History
DepositionApr 25, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64375.png

Downloads & links

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Map

FileDownload / File: emd_64375.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0895
Minimum - Maximum-1.1574113 - 2.0037026
Average (Standard dev.)0.000515545 (±0.033688005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64375_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64375_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : the hexamer of the Xenopus IgX-Fc

EntireName: the hexamer of the Xenopus IgX-Fc
Components
  • Complex: the hexamer of the Xenopus IgX-Fc
    • Protein or peptide: Uncharacterized LOC101027262 precursor

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Supramolecule #1: the hexamer of the Xenopus IgX-Fc

SupramoleculeName: the hexamer of the Xenopus IgX-Fc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Uncharacterized LOC101027262 precursor

MacromoleculeName: Uncharacterized LOC101027262 precursor / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 23.912041 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLQVYPLTPT FHDLYFSRNA KITCLVSSMK TIENFDISWE REKAGNLEFV TEDPVLHDNG TYSVASILSV CAEDWESGDK FSCTVRSQD LPSPVKKTIF KQNEGTPKAP DVYLLPPSAQ ELIQQEMVTL ICFVTGFNPK EIFIQWMQGG VSISEDKFIN T VPMKSDGE ...String:
NLQVYPLTPT FHDLYFSRNA KITCLVSSMK TIENFDISWE REKAGNLEFV TEDPVLHDNG TYSVASILSV CAEDWESGDK FSCTVRSQD LPSPVKKTIF KQNEGTPKAP DVYLLPPSAQ ELIQQEMVTL ICFVTGFNPK EIFIQWMQGG VSISEDKFIN T VPMKSDGE QTYFIYSKLA IPAAKWNQGD VFTCVVGHEA LPLYITQQSI DKSSG

UniProtKB: Uncharacterized LOC101027262 precursor

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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 POLARA 300
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.4000000000000001 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44566
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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