› 6lbe

X-ray diffraction
2.6Å resolution

Crystal structure of bony fish MHC class I binding beta2M-2 for 2.6 angstrom

Released:
DOI: 10.2210/pdb6lbe/pdb
PDB entry 6lbe coloured by chain, front view.
PDB entry 6lbe coloured by chain, side view.
PDB entry 6lbe 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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-104872 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chains: A, C
Molecule details ›
Chains: A, C
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:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 99 amino acids
Theoretical weight: 11.4 KDa
Source organism: Ctenopharyngodon idella
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A3G2VUI3 (Residues: 20-117; Coverage: 100%)
Gene name: b2m-b
Sequence domains: Immunoglobulin C1-set domain
RNA-directed RNA polymerase L Chains: E, F
Molecule details ›
Chains: E, F
Length: 9 amino acids
Theoretical weight: 1.09 KDa
Source organism: synthetic construct
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: SSRF BEAMLINE BL19U1
Spacegroup: P1
Unit cell:
a: 53.19Å b: 65.27Å c: 69.71Å
α: 64.94° β: 75.67° γ: 73.61°
R-values:
R R work R free
0.173 0.169 0.254
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)
6 other articles

1 mention without citation

The Mechanism of β2m Molecule-Induced Changes in the Peptide Presentation Profile in a Bony Fish.
Li et al. (2020)