› 7y09

Electron Microscopy
3.71Å resolution

Cryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of DBLMSP

Released:
DOI: 10.2210/pdb7y09/pdb
PDB entry 7y09 coloured by chain, front view.
PDB entry 7y09 coloured by chain, side view.
PDB entry 7y09 coloured by chain, top view.
Source organisms:
Primary publication:
Plasmodium falciparum has evolved multiple mechanisms to hijack human immunoglobulin M.
Ji C, Shen H, Su C, Li Y, Chen S, Sharp TH, Xiao J
OpenAccess logo Nat Commun 14 2650 (2023)
PMID: 37156765
Related structures: EMD-33538

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-111502 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Duffy-antigen binding domain-containing protein Chain: R
Molecule details ›
Chain: R
Length: 656 amino acids
Theoretical weight: 75.11 KDa
Source organism: Plasmodium falciparum
Expression system: Homo sapiens
UniProt:
  • Canonical: C5HX06 (Residues: 1-656; Coverage: 100%)
Sequence domains:
Immunoglobulin heavy constant mu Chains: A, B, C, D, E, F, G, H, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, K, L
Length: 383 amino acids
Theoretical weight: 41.88 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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
Molecule details ›
Chain: J
Length: 136 amino acids
Theoretical weight: 15.48 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01591 (Residues: 24-159; Coverage: 99%)
Gene names: IGCJ, IGJ, JCHAIN
Sequence domains: Immunoglobulin J chain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 10 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.71Å
Relevant EMDB volumes: EMD-33538
Expression system: Homo sapiens

Quick links

Citations

1 citations in other articles

Cryo-electron microscopy of IgM-VAR2CSA complex reveals IgM inhibits binding of Plasmodium falciparum to Chondroitin Sulfate A.
Akhouri et al. (2023)