7K0C | pdb_00007k0c

Structure of Secretory IgM Core


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7K0C

This is version 1.4 of the entry. See complete history

Literature

Structure of the human secretory immunoglobulin M core.

Kumar, N.Arthur, C.P.Ciferri, C.Matsumoto, M.L.

(2021) Structure 29: 564-571.e3

  • DOI: https://doi.org/10.1016/j.str.2021.01.002
  • Primary Citation Related Structures: 
    7K0C

  • PubMed Abstract: 

    Immunoglobulins (Ig) A and M are the only human antibodies that form oligomers and undergo transcytosis to mucosal secretions via the polymeric Ig receptor (pIgR). When complexed with the J-chain (JC) and the secretory component (SC) of pIgR, secretory IgA and IgM (sIgA and sIgM) play critical roles in host-pathogen defense. Recently, we determined the structure of sIgA-Fc which elucidated the mechanism of polymeric IgA assembly and revealed an extensive binding interface between IgA-Fc, JC, and SC. Despite low sequence identity shared with IgA-Fc, IgM-Fc also undergoes JC-mediated assembly and binds pIgR. Here, we report the structure of sIgM-Fc and carryout a systematic comparison to sIgA-Fc. Our structural analysis reveals a remarkably conserved mechanism of JC-templated oligomerization and SC recognition of both IgM and IgA through a highly conserved network of interactions. These studies reveal the structurally conserved features of sIgM and sIgA required for function in mucosal immunity.


  • Organizational Affiliation
    • Department of Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 487.97 kDa 
  • Atom Count: 22,540 
  • Modeled Residue Count: 2,898 
  • Deposited Residue Count: 4,418 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polymeric immunoglobulin receptorA [auth C]591Homo sapiensMutation(s): 0 
Gene Names: PIGR
UniProt & NIH Common Fund Data Resources
Find proteins for P01833 (Homo sapiens)
Explore P01833 
Go to UniProtKB:  P01833
PHAROS:  P01833
GTEx:  ENSG00000162896 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01833
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin heavy constant mu369Homo sapiensMutation(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
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin J chainJ [auth D]137Homo sapiensMutation(s): 0 
Gene Names: JCHAINIGCJIGJ
UniProt & NIH Common Fund Data Resources
Find proteins for P01591 (Homo sapiens)
Explore P01591 
Go to UniProtKB:  P01591
PHAROS:  P01591
GTEx:  ENSG00000132465 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01591
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01591-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcisTEM

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2021-06-16
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2025-05-28
    Changes: Data collection