› 8rbv

X-ray diffraction
1.8Å resolution

SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL) presented by HLA-A*02:01

Released:
DOI: 10.2210/pdb8rbv/pdb
PDB entry 8rbv coloured by chain, front view.
PDB entry 8rbv coloured by chain, side view.
PDB entry 8rbv coloured by chain, top view.
Source organisms:
Primary publication:
The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific.
Ahn YM, Maddumage JC, Grant EJ, Chatzileontiadou DSM, Perera WWJG, Baker BM, Szeto C, Gras S
Curr Res Struct Biol 7 100148 (2024)
PMID: 38742159

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-144169 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 365 amino acids
Theoretical weight: 40.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q53Z42 (Residues: 1-365; Coverage: 100%)
Gene name: HLA-A
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 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Spike protein S2' Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.03 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTC2 (Residues: 976-984; Coverage: 1%)
Gene names: 2, S

Ligands and Environments

4 bound ligands:
Ligand ACT 2 x ACT
Ligand EDO 2 x EDO
Ligand CD 2 x CD
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 59.821Å b: 78.177Å c: 110.911Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.18 0.211
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

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