9UO6 | pdb_00009uo6

Cryo-EM structure of the Xenopus IgX-Fc hexamer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Xenopus IgX informs engineering strategies of IgM and IgG hexamers.

Zhang, R.Ji, C.Li, S.Li, N.Gao, N.Xiao, J.

(2025) Sci Adv 11: eaea3737-eaea3737

  • DOI: https://doi.org/10.1126/sciadv.aea3737
  • Primary Citation of Related Structures:  
    9UO3, 9UO4, 9UO5, 9UO6

  • PubMed 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), Xenopus laevis 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.


  • Organizational Affiliation
    • Biomedical Pioneering Innovation Center (BIOPIC), State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking University, Beijing, P.R. China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized LOC101027262 precursor213Xenopus laevisMutation(s): 0 
Gene Names: LOC101027262
UniProt
Find proteins for Q6INK3 (Xenopus laevis)
Explore Q6INK3 
Go to UniProtKB:  Q6INK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6INK3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release