› 3vcl

X-ray diffraction
1.7Å resolution

Crystal Structure of HLA-B7 with the HCMV pp65 peptide RPHERNGFTVL

Released:
DOI: 10.2210/pdb3vcl/pdb
PDB entry 3vcl coloured by chain, front view.
PDB entry 3vcl coloured by chain, side view.
PDB entry 3vcl coloured by chain, top view.
Source organisms:
Primary publication:
The impact of a large and frequent deletion in the human TCR β locus on antiviral immunity.
Brennan RM, Petersen J, Neller MA, Miles JJ, Burrows JM, Smith C, McCluskey J, Khanna R, Rossjohn J, Burrows SR
J Immunol 188 2742-8 (2012)
PMID: 22323539

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-135250 (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: 275 amino acids
Theoretical weight: 31.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01889 (Residues: 25-299; Coverage: 81%)
Gene names: HLA-B, HLAB
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
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
65 kDa phosphoprotein Chain: C
Molecule details ›
Chain: C
Length: 11 amino acids
Theoretical weight: 1.33 KDa
Source organism: Human betaherpesvirus 5
Expression system: Not provided
UniProt:
  • Canonical: Q6SW59 (Residues: 265-275; Coverage: 2%)
Gene name: UL83

Ligands and Environments

2 bound ligands:
Ligand NI 4 x NI
Ligand GOL 8 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P41212
Unit cell:
a: 65.786Å b: 65.786Å c: 237.107Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.217
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Classical and non-classical MHC I molecule manipulation by human cytomegalovirus: so many targets—but how many arrows in the quiver?
Halenius et al. (2015)
2 more

22 mentions without citation

Screening and structure-based modeling of T-cell epitopes of Nipah virus proteome: an immunoinformatic approach for designing peptide-based vaccine.
Kamthania et al. (2015)
21 more