› 5h5z

X-ray diffraction
1.74Å resolution

Crystal structure of bony fish MHC class I, peptide and B2m II

Released:
DOI: 10.2210/pdb5h5z/pdb
PDB entry 5h5z coloured by chain, front view.
PDB entry 5h5z coloured by chain, side view.
PDB entry 5h5z coloured by chain, top view.
Source organisms:
Primary publication:
The Mechanism of β2m Molecule-Induced Changes in the Peptide Presentation Profile in a Bony Fish.
Li Z, Zhang N, Ma L, Zhang L, Meng G, Xia C
iScience 23 101119 (2020)
PMID: 32438322

Function and Biology Details

Reactions catalysed: 
(1a) S-adenosyl-L-methionine + G(5')pppAACA-[mRNA] = S-adenosyl-L-homocysteine + G(5')pppAmACA-[mRNA]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
(1a) (5')pppAACA-[mRNA] + (protein L)-L-histidine = diphosphate + (protein L)-L-histidyl-(5')phosphonato-AACA-[mRNA] + H(2)O
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179233 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 275 amino acids
Theoretical weight: 31.45 KDa
Source organism: Ctenopharyngodon idella
Expression system: Escherichia coli
UniProt:
  • Canonical: Q65XY8 (Residues: 17-291; Coverage: 85%)
Gene name: UAA106
Sequence domains:
Structure domains:
Ig-like domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 98 amino acids
Theoretical weight: 11.32 KDa
Source organism: Ctenopharyngodon idella
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6L7B0 (Residues: 20-116; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
RNA-directed RNA polymerase L Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.09 KDa
Source organism: Sprivivirus cyprinus
Expression system: Not provided
UniProt:
  • Canonical: Q91DR9 (Residues: 828-836; Coverage: 0%)
Gene name: L

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2
Unit cell:
a: 119.35Å b: 50.65Å c: 90.31Å
α: 90° β: 129.37° γ: 90°
R-values:
R R work R free
0.173 0.171 0.204
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Peptide-dependent tuning of major histocompatibility complex motional properties and the consequences for cellular immunity.
Ayres et al. (2022)
4 other articles

4 mentions without citation

Structure and Peptidome of the Bat MHC Class I Molecule Reveal a Novel Mechanism Leading to High-Affinity Peptide Binding.
Qu et al. (2019)
3 more