› 8wys

Electron Microscopy
3.41Å resolution

Local map of human CD5L bound to IgM-Fc/J

Released:
DOI: 10.2210/pdb8wys/pdb
PDB entry 8wys coloured by chain, front view.
PDB entry 8wys coloured by chain, side view.
PDB entry 8wys coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
CD5L associates with IgM via the J chain.
Wang Y, Su C, Ji C, Xiao J
Nat Commun 15 8397 (2024)
PMID: 39333069
Related structures: EMD-37937

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-271727 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Immunoglobulin heavy constant mu; Interleukin-2 Chains: A, L
Molecule details ›
Chains: A, L
Length: 403 amino acids
Theoretical weight: 44.09 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P60568 (Residues: 1-21; Coverage: 1%)
  • Canonical: P01871 (Residues: 106-433; Coverage: 69%)
Gene names: IGHM, IL2
Sequence domains: Immunoglobulin C1-set domain
CD5 antigen-like; Interleukin-2 Chain: M
Molecule details ›
Chain: M
Length: 359 amino acids
Theoretical weight: 39.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P60568 (Residues: 1-21; Coverage: 1%)
  • Canonical: O43866 (Residues: 20-347; Coverage: 100%)
Gene names: API6, CD5L, IL2, UNQ203/PRO229
Sequence domains: Scavenger receptor cysteine-rich domain
Immunoglobulin J chain Chain: J

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.41Å
Relevant EMDB volumes: EMD-37937
Expression system: Homo sapiens

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