› 4u1m

X-ray diffraction
1.18Å resolution

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

Released:
DOI: 10.2210/pdb4u1m/pdb
PDB entry 4u1m coloured by chain, front view.
PDB entry 4u1m coloured by chain, side view.
PDB entry 4u1m 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 Chain: A
Molecule details ›
Chain: A
Length: 277 amino acids
Theoretical weight: 32.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01889 (Residues: 25-301; Coverage: 82%)
Gene names: HLA-B, HLAB
Sequence domains:
Structure 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
Structure domains: Immunoglobulins
C-terminal core protein Chain: C
Molecule details ›
Chain: C
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

2 bound ligands:
Ligand EDO 26 x EDO
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 51.06Å b: 81.34Å c: 110.93Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.162 0.18
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)