› 7m8u

X-ray diffraction
1.45Å resolution

Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from SARS-CoV-2 spike (S896-904)

Released:
DOI: 10.2210/pdb7m8u/pdb
PDB entry 7m8u coloured by chain, front view.
PDB entry 7m8u coloured by chain, side view.
PDB entry 7m8u 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-144171 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 277 amino acids
Theoretical weight: 32.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q546I9 (Residues: 25-301; Coverage: 82%)
Gene name: HLA-B
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(DE3)
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: 1.07 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTC2 (Residues: 896-904; Coverage: 1%)
Gene names: 2, S

Ligands and Environments

2 bound ligands:
Ligand PO4 2 x PO4
Ligand NA 3 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 51.238Å b: 82.38Å c: 111.011Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.229
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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