› 5hgd

X-ray diffraction
2.07Å resolution

HLA*A2402 complexed with HIV nef138 Y2F mutant 10mer epitope

Released:
DOI: 10.2210/pdb5hgd/pdb
PDB entry 5hgd coloured by chain, front view.
PDB entry 5hgd coloured by chain, side view.
PDB entry 5hgd coloured by chain, top view.
Source organisms:
Primary publication:
Effects of a Single Escape Mutation on T Cell and HIV-1 Co-adaptation.
Sun X, Shi Y, Akahoshi T, Fujiwara M, Gatanaga H, Schönbach C, Kuse N, Appay V, Gao GF, Oka S, Takiguchi M
Cell Rep 15 2279-2291 (2016)
PMID: 27239036

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-137651 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, A alpha chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 275 amino acids
Theoretical weight: 31.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P04439 (Residues: 25-298; Coverage: 80%)
Gene names: HLA-A, HLAA
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-Gold(DE3)pLysS AG'
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: 10 amino acids
Theoretical weight: 1.27 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P04601 (Residues: 134-143; Coverage: 5%)
Gene name: nef

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P1
Unit cell:
a: 50.655Å b: 65.741Å c: 87.519Å
α: 67.97° β: 89.8° γ: 89.89°
R-values:
R R work R free
0.186 0.184 0.224
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

2 review citations

Designs of Antigen Structure and Composition for Improved Protein-Based Vaccine Efficacy.
Saylor et al. (2020)
1 more