› 6m2j

X-ray diffraction
2.2Å resolution

Uncommon structural features of rabbit MHC class I (RLA-A1) complexed with rabbit haemorrhagic disease virus (RHDV) derived peptide, VP60-1

Released:
DOI: 10.2210/pdb6m2j/pdb
PDB entry 6m2j coloured by chain, front view.
PDB entry 6m2j coloured by chain, side view.
PDB entry 6m2j coloured by chain, top view.
Source organisms:
Primary publication:
Strict Assembly Restriction of Peptides from Rabbit Hemorrhagic Disease Virus Presented by Rabbit Major Histocompatibility Complex Class I Molecule RLA-A1.
Zhang Q, Liu K, Yue C, Zhang D, Lu D, Xiao W, Liu P, Zhao Y, Gao G, Ding C, Lyu J, Liu WJ
J Virol 94 (2020)
PMID: 32522857

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-138884 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
RLA class I histocompatibility antigen, alpha chain 19-1 Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 31.68 KDa
Source organism: Oryctolagus cuniculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P06140 (Residues: 25-298; Coverage: 81%)
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Capsid protein VP60 Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.03 KDa
Source organism: Rabbit hemorrhagic disease virus
Expression system: Not provided
UniProt:
  • Canonical: P27410 (Residues: 2308-2316; Coverage: 0%)
Gene name: ORF1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 49.625Å b: 74.361Å c: 155.669Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.202 0.256
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

New vistas unfold: Chicken MHC molecules reveal unexpected ways to present peptides to the immune system.
Halabi et al. (2022)
3 other articles

1 mention without citation

Strict Assembly Restriction of Peptides from Rabbit Hemorrhagic Disease Virus Presented by Rabbit Major Histocompatibility Complex Class I Molecule RLA-A1.
Zhang et al. (2020)