9P6V | pdb_00009p6v

Cryo-EM structure of chimeric immunoglobulin M comprising bony fish and human sequences, hFcm-tFcm-chi4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9P6V

This is version 1.0 of the entry. See complete history

Literature

Chimeric Immunoglobulin and human Immunoglobulin M structures provide insights on joining-chain independent assembly and function.

Lyu, M.Stadtmueller, B.M.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.07.09.663956
  • Primary Citation Related Structures: 
    9P6U, 9P6V

  • PubMed Abstract: 

    Polymeric (p) immunoglobulins (Igs) play critical roles in vertebrate immunity. IgM is the evolutionarily oldest pIg and functions both in circulation and in the mucosa. pIgM typically comprises between four and six IgM monomers and up to one joining chain (JC), which in mammals facilitates pIg assembly and promotes delivery to mucosal secretions. Bony fish (teleosts) lack JC and assemble tetrameric IgM whereas humans can express JC-containing pentamers and JC-free hexamers. Here we report cryo-electron microscopy structures of two JC-free chimeric IgM, comprising bony fish and human sequences, and the structure of human hexameric IgM. Chimeric IgM structures adopted unique pentameric geometry distinct from both human and fish pIgM whereas the human hexameric IgM structure adopted hexagonal geometry similar to JC-containing pentameric IgM, albeit with structural differences in center of the molecule. Together results provide new insights on how IgM heavy chain motifs contribute to JC-free pIgM assembly and reveal plasticity of this process, which can be manipulated to create pIg structures not observed in nature. Moreover, we found that antigen-targeting chimeric IgM could neutralize C. difficile toxin cytotoxicity, indicating potential to engineer uniquely structured pIgs to prevent or treat disease.


  • Organizational Affiliation
    • Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA.

Macromolecule Content 

  • Total Structure Weight: 268.46 kDa 
  • Atom Count: 16,799 
  • Modeled Residue Count: 2,150 
  • Deposited Residue Count: 2,410 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chimeric Immunoglobulin heavy constant mu241Homo sapiensOncorhynchus mykiss
This entity is chimeric
Mutation(s): 0 
Gene Names: IGHM
UniProt & NIH Common Fund Data Resources
Find proteins for P01871 (Homo sapiens)
Explore P01871 
Go to UniProtKB:  P01871
PHAROS:  P01871
GTEx:  ENSG00000211899 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01871
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.7
MODEL REFINEMENTPHENIX1.21

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI165570

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release