› 8cmh

X-ray diffraction
1.64Å resolution

Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S486-505

Released:
DOI: 10.2210/pdb8cmh/pdb
PDB entry 8cmh coloured by chain, front view.
PDB entry 8cmh coloured by chain, side view.
PDB entry 8cmh coloured by chain, top view.
Source organisms:
Primary publication:
Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4+ T cell immunity.
Chen Y, Mason GH, Scourfield DO, Greenshields-Watson A, Haigh TA, Sewell AK, Long HM, Gallimore AM, Rizkallah P, MacLachlan BJ, Godkin A
OpenAccess logo Cell Rep 42 112827 (2023)
PMID: 37471227

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-270204 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class II histocompatibility antigen, DR alpha chain Chain: A
Molecule details ›
Chain: A
Length: 183 amino acids
Theoretical weight: 21.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01903 (Residues: 26-207; Coverage: 80%)
Gene names: HLA-DRA, HLA-DRA1
Sequence domains:
Ig-like domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 194 amino acids
Theoretical weight: 22.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D7RIG0 (Residues: 30-219; Coverage: 80%)
Gene name: HLA-DRB1
Sequence domains:
Spike protein S1 Chain: C
Molecule details ›
Chain: C
Length: 20 amino acids
Theoretical weight: 2.41 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTC2 (Residues: 486-505; Coverage: 2%)
Gene names: 2, S

Ligands and Environments

3 bound ligands:
Ligand EDO 30 x EDO
Ligand SO4 1 x SO4
Ligand DHL 1 x DHL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21212
Unit cell:
a: 91.034Å b: 120.186Å c: 40.879Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.208
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 citation in other articles

De novo design of anti-variant COVID-19 vaccine.
Goswami et al. (2023)
1 more

2 mentions without citation

The efficacy of high-flow nasal cannula (HFNC) versus non-invasive ventilation (NIV) in patients at high risk of extubation failure: a systematic review and meta-analysis.
Wang et al. (2023)
1 more