8GHZ | pdb_00008ghz

Cryo-EM structure of fish immunogloblin M-Fc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The structure of the teleost Immunoglobulin M core provides insights on polymeric antibody evolution, assembly, and function.

Lyu, M.Malyutin, A.G.Stadtmueller, B.M.

(2023) Nat Commun 14: 7583-7583

  • DOI: https://doi.org/10.1038/s41467-023-43240-z
  • Primary Citation Related Structures: 
    8GHZ

  • PubMed Abstract: 

    Polymeric (p) immunoglobulins (Igs) serve broad functions during vertebrate immune responses. Typically, pIgs contain between two and six Ig monomers, each with two antigen binding fragments and one fragment crystallization (Fc). In addition, many pIgs assemble with a joining-chain (JC); however, the number of monomers and potential to include JC vary with species and heavy chain class. Here, we report the cryo-electron microscopy structure of IgM from a teleost (t) species, which does not encode JC. The structure reveals four tIgM Fcs linked through eight C-terminal tailpieces (Tps), which adopt a single β-sandwich-like domain (Tp assembly) located between two Fcs. Specifically, two of eight heavy chains fold uniquely, resulting in a structure distinct from mammalian IgM, which typically contains five IgM monomers, one JC and a centrally-located Tp assembly. Together with mutational analysis, structural data indicate that pIgs have evolved a range of assembly mechanisms and structures, each likely to support unique antibody effector functions.


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

Macromolecule Content 

  • Total Structure Weight: 220.68 kDa 
  • Atom Count: 14,390 
  • Modeled Residue Count: 1,768 
  • Deposited Residue Count: 1,896 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Teleost immunoglobulin M protein
A, B, C, D, E
A, B, C, D, E, F, G, H
237Oncorhynchus mykissMutation(s): 0 
UniProt
Find proteins for A0A8C7NK04 (Oncorhynchus mykiss)
Explore A0A8C7NK04 
Go to UniProtKB:  A0A8C7NK04
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8C7NK04
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, J, K, L, M
I, J, K, L, M, N, O, P
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0

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: 2023-11-08
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary