› 8r84

Electron Microscopy
3.6Å resolution

pentameric IgMFc-AIM complex focused refinement

Released:
DOI: 10.2210/pdb8r84/pdb
PDB entry 8r84 coloured by chain, front view.
PDB entry 8r84 coloured by chain, side view.
PDB entry 8r84 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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 PB
Nat Commun 15 9387 (2024)
PMID: 39477921
Related structures: EMD-18994

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-283165 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
CD5 antigen-like Chain: N
Molecule details ›
Chain: N
Length: 328 amino acids
Theoretical weight: 36.1 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: O43866 (Residues: 20-347; Coverage: 100%)
Gene names: API6, CD5L, UNQ203/PRO229
Sequence domains: Scavenger receptor cysteine-rich domain
Immunoglobulin heavy constant mu Chains: A, B, K, L
Molecule details ›
Chains: A, B, K, L
Length: 361 amino acids
Theoretical weight: 39.72 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P01871 (Residues: 106-433; Coverage: 69%)
  • Best match: P01871-1 (Residues: 106-453)
Gene name: IGHM
Sequence domains: Immunoglobulin C1-set domain
Immunoglobulin J chain Chain: J

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-18994
Expression system: Cricetulus griseus

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