› 3e6f

X-ray diffraction
2.41Å resolution

MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide, PA9, from the Human immunodeficiency virus (BaL) envelope glycoprotein 120

Released:
DOI: 10.2210/pdb3e6f/pdb
PDB entry 3e6f coloured by chain, front view.
PDB entry 3e6f coloured by chain, side view.
PDB entry 3e6f coloured by chain, top view.
Source organisms:
Primary publication:
Different vaccine vectors delivering the same antigen elicit CD8+ T cell responses with distinct clonotype and epitope specificity.
Honda M, Wang R, Kong WP, Kanekiyo M, Akahata W, Xu L, Matsuo K, Natarajan K, Robinson H, Asher TE, Price DA, Douek DC, Margulies DH, Nabel GJ
J Immunol 183 2425-34 (2009)
PMID: 19620307

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-135032 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, D-D alpha chain Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 31.95 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01900 (Residues: 26-298; Coverage: 80%)
Gene name: H2-D1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.68 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Surface protein gp120 Chain: P
Molecule details ›
Chain: P
Length: 9 amino acids
Theoretical weight: 952 Da
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P05878 (Residues: 309-317; Coverage: 1%)
Gene name: env

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21212
Unit cell:
a: 67.81Å b: 109.515Å c: 53.762Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.25 0.223 0.271
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Human immunodeficiency virus (HIV) immunopathogenesis and vaccine development: a review.
Girard et al. (2011)
4 more

3 mentions without citation

Roles for major histocompatibility complex glycosylation in immune function.
Ryan et al. (2012)
2 more