› 7m8s

X-ray diffraction
2.35Å resolution

Crystal Structure of HLA-A*02:01 in complex with KLNDLCFTNV, an 10-mer epitope from SARS-CoV-2 Spike (S386-395)

Released:
DOI: 10.2210/pdb7m8s/pdb
PDB entry 7m8s coloured by chain, front view.
PDB entry 7m8s coloured by chain, side view.
PDB entry 7m8s coloured by chain, top view.
Source organisms:
Primary publication:
SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules
Nguyen AT, Szeto C, Jayasinghe D, Lobos CA, Halim H, Chatzileontiadou DSM, Grant EJ, Gras S
Biophysica 1 (2021)

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-102960 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chains: A, D
Molecule details ›
Chains: A, D
Length: 276 amino acids
Theoretical weight: 31.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A140T913 (Residues: 25-300; Coverage: 80%)
Gene name: HLA-A
Sequence domains:
Beta-2-microglobulin Chains: B, E
Molecule details ›
Chains: B, E
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Spike protein S1 Chains: C, F
Molecule details ›
Chains: C, F
Length: 10 amino acids
Theoretical weight: 1.17 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTC2 (Residues: 386-395; Coverage: 1%)
Gene names: 2, S

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 64.601Å b: 86.686Å c: 163.207Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.197 0.248
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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