› 1sje

X-ray diffraction
2.45Å resolution

HLA-DR1 complexed with a 16 residue HIV capsid peptide bound in a hairpin conformation

Released:
DOI: 10.2210/pdb1sje/pdb
PDB 1sje coloured by chain and viewed from the front.
PDB 1sje coloured by chain and viewed from the side.
PDB 1sje coloured by chain and viewed from the top.
Source organisms:
Primary publication:
A hairpin turn in a class II MHC-bound peptide orients residues outside the binding groove for T cell recognition.
Zavala-Ruiz Z, Strug I, Walker BD, Norris PJ, Stern LJ
Proc Natl Acad Sci U S A 101 13279-84 (2004)
PMID: 15331779

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
HLA class II histocompatibility antigen, DR alpha chain Chain: A
Molecule details ›
Chain: A
Length: 180 amino acids
Theoretical weight: 20.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01903 (Residues: 28-207; Coverage: 79%)
Gene names: HLA-DRA, HLA-DRA1
Structure domains:
HLA class II histocompatibility antigen, DRB1 beta chain Chain: B
Molecule details ›
Chain: B
Length: 190 amino acids
Theoretical weight: 22.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01911 (Residues: 30-219; Coverage: 80%)
Gene name: HLA-DRB1
Structure domains:
Capsid protein p24 Chain: C
Molecule details ›
Chain: C
Length: 16 amino acids
Theoretical weight: 1.65 KDa
Source organism: Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
Expression system: Not provided
UniProt:
  • Canonical: P12495 (Residues: 167-182; Coverage: 3%)
Gene name: gag
Enterotoxin type C-3 Chain: D
Molecule details ›
Chain: D
Length: 239 amino acids
Theoretical weight: 27.72 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0L5 (Residues: 28-266; Coverage: 100%)
Gene name: entC3
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: OTHER
Spacegroup: R3
Unit cell:
a: 172.746Å b: 172.746Å c: 121.399Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.198 0.196 0.223
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided
  • Escherichia coli

Quick links

Citations

5 review citations

From Chickens to Humans: The Importance of Peptide Repertoires for MHC Class I Alleles.
Kaufman J. (2020)
4 more

11 mentions without citation

Model for the peptide-free conformation of class II MHC proteins.
Painter et al. (2008)
10 more