8R84

pentameric IgMFc-AIM complex focused refinement

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Cricetulus griseus
  • Mutation(s): No 

  • Deposited: 2023-11-28 Released: 2024-11-06 
  • Deposition Author(s): Chen, Q., Arai, S., Miyazaki, T., Rosenthal, P.
  • Funding Organization(s): Cancer Research UK, Medical Research Council (MRC, United Kingdom), Wellcome Trust, Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM reveals structural basis for human AIM/CD5L recognition of polymeric immunoglobulin M.

Chen, Q.Ishii, K.Mori, H.Nishijima, A.Arai, S.Miyazaki, T.Rosenthal, P.B.

(2024) Nat Commun 15: 9387-9387

  • DOI: https://doi.org/10.1038/s41467-024-53615-5
  • Primary Citation of Related Structures:  
    8R83, 8R84

  • PubMed Abstract: 

    Cell surface scavenger receptors contribute to homoeostasis and the response to pathogens and products associated with damage by binding to common molecular features on a wide range of targets. Apoptosis inhibitor of macrophage (AIM/CD5L) is a soluble protein belonging to the scavenger receptor cysteine-rich (SRCR) superfamily that contributes to prevention of a wide range of diseases associated with infection, inflammation, and cancer. AIM forms complexes with IgM pentamers which helps maintain high-levels of circulating AIM in serum for subsequent activation on release from the complex. The structural basis for AIM recognition of IgM as well as other binding targets is unknown. Here we apply cryogenic electron microscopy imaging (cryo-EM) to show how interfaces on both of AIM's C-terminal SRCR domains interact with the Fcμ constant region and J chain components of the IgM core. Both SRCR interfaces are also shown to contribute interactions important for AIM binding to damage-associated molecular patterns (DAMPs).


  • Organizational Affiliation

    Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CD5 antigen-likeA [auth N]328Homo sapiensMutation(s): 0 
Gene Names: CD5L
UniProt & NIH Common Fund Data Resources
Find proteins for O43866 (Homo sapiens)
Explore O43866 
Go to UniProtKB:  O43866
PHAROS:  O43866
GTEx:  ENSG00000073754 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43866
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ig-like domain-containing proteinB,
C [auth L],
D [auth K],
E [auth A]
361Homo sapiensMutation(s): 0 
UniProt
Find proteins for A0A7N5JWI9 (Ailuropoda melanoleuca)
Explore A0A7N5JWI9 
Go to UniProtKB:  A0A7N5JWI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7N5JWI9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin J chainF [auth J]169Homo sapiensMutation(s): 0 
Gene Names: JCHAIN
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 Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--
Medical Research Council (MRC, United Kingdom)United Kingdom--
Wellcome TrustUnited Kingdom--
Japan Agency for Medical Research and Development (AMED)Japan--
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-27
    Changes: Data collection