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Crystal structure of HLA-A*11:01 in complex with SVLNDILARL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)

X-ray diffraction
2.7Å resolution
PDB entry 8rbu coloured by chain, front view.
PDB entry 8rbu coloured by chain, side view.
PDB entry 8rbu coloured by chain, top view.
Source organisms:
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero trimer
Accessible surface area: 18308.45 Å2
Buried surface area: 7745.06 Å2
Dissociation area: 1,084.47 Å2
Dissociation energy (ΔGdiss): 5.25 kcal/mol
Dissociation entropy (TΔSdiss): 7.66 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-272806

Macromolecules

Ig-like domain-containing protein
Chain: A
Length: 365 amino acids
Theoretical weight: 40.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q5S3G3 (Residues: 1-365; Coverage: 100%)
Gene name: HLA-A
Pfam:
Ig-like domain-containing protein in PDB entry 8rbu, assembly 1, front view.
Ig-like domain-containing protein in PDB entry 8rbu, assembly 1, side view.
Ig-like domain-containing protein in PDB entry 8rbu, assembly 1, top view.
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Beta-2-microglobulin
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
Pfam: Immunoglobulin C1-set domain
Beta-2-microglobulin in PDB entry 8rbu, assembly 1, front view.
Beta-2-microglobulin in PDB entry 8rbu, assembly 1, side view.
Beta-2-microglobulin in PDB entry 8rbu, assembly 1, top view.
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Spike protein S2'
Chain: C
Length: 10 amino acids
Theoretical weight: 1.11 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTC2 (Residues: 975-984; Coverage: 1%)
Gene names: 2, S
Spike protein S2' in PDB entry 8rbu, assembly 1, front view.
Spike protein S2' in PDB entry 8rbu, assembly 1, side view.
Spike protein S2' in PDB entry 8rbu, assembly 1, top view.
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