› 5gsd

X-ray diffraction
2.3Å resolution

Crystal structure of LMP2 peptide from EBV in complex with HLA-A*11:01

Released:
DOI: 10.2210/pdb5gsd/pdb
PDB entry 5gsd coloured by chain, front view.
PDB entry 5gsd coloured by chain, side view.
PDB entry 5gsd coloured by chain, top view.
Source organisms:
Primary publication:
Dual non-contiguous peptide occupancy of HLA class I evoke antiviral human CD8 T cell response and form neo-epitopes with self-antigens.
Xiao Z, Ye Z, Tadwal VS, Shen M, Ren EC
Sci Rep 7 5072 (2017)
PMID: 28698575

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-137664 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, A alpha chain Chain: A
Molecule details ›
Chain: A
Length: 275 amino acids
Theoretical weight: 31.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04439 (Residues: 25-299; Coverage: 81%)
Gene names: HLA-A, HLAA
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.75 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
Latent membrane protein 2 Chain: C
Molecule details ›
Chain: C
Length: 7 amino acids
Theoretical weight: 722 Da
Source organism: synthetic construct
Expression system: Not provided
UniProt:
  • Canonical: P13285 (Residues: 343-349; Coverage: 1%)
Gene name: LMP2

Ligands and Environments

1 bound ligand:
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER AXS MICROSTAR
Spacegroup: P212121
Unit cell:
a: 55.353Å b: 67.646Å c: 115.603Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.195 0.273
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 citation in other articles

Antigen processing and presentation in HIV infection.
Boucau et al. (2018)
3 more

1 mention without citation

Dual non-contiguous peptide occupancy of HLA class I evoke antiviral human CD8 T cell response and form neo-epitopes with self-antigens.
Xiao et al. (2017)