› 4u1k

X-ray diffraction
2.09Å resolution

HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes

Released:
DOI: 10.2210/pdb4u1k/pdb
PDB entry 4u1k coloured by chain, front view.
PDB entry 4u1k coloured by chain, side view.
PDB entry 4u1k coloured by chain, top view.
Source organisms:
Primary publication:
A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape.
Kløverpris HN, Cole DK, Fuller A, Carlson J, Beck K, Schauenburg AJ, Rizkallah PJ, Buus S, Sewell AK, Goulder P
Retrovirology 12 20 (2015)
PMID: 25808313

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-135139 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, B alpha chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 277 amino acids
Theoretical weight: 32.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01889 (Residues: 25-300; Coverage: 82%)
Gene names: HLA-B, HLAB
Sequence domains:
Structure 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
Structure domains: Immunoglobulins
C-terminal core protein Chains: C, F
Molecule details ›
Chains: C, F
Length: 9 amino acids
Theoretical weight: 1.1 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P03407 (Residues: 75-83; Coverage: 4%)
Gene name: nef

Ligands and Environments

3 bound ligands:
Ligand GOL 8 x GOL
Ligand EDO 6 x EDO
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P1
Unit cell:
a: 46.27Å b: 49.13Å c: 107.46Å
α: 91.37° β: 93.57° γ: 95.75°
R-values:
R R work R free
0.178 0.176 0.226
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Role of HLA Adaptation in HIV Evolution.
Kløverpris et al. (2015)
2 more

1 mention without citation

A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape.
Kløverpris et al. (2015)