› 5ksu

X-ray diffraction
2.73Å resolution

Crystal structure of HLA-DQ2.5-CLIP1 at 2.73 resolution

Released:
DOI: 10.2210/pdb5ksu/pdb
PDB entry 5ksu coloured by chain, front view.
PDB entry 5ksu coloured by chain, side view.
PDB entry 5ksu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Unraveling the structural basis for the unusually rich association of human leukocyte antigen DQ2.5 with class-II-associated invariant chain peptides.
Nguyen TB, Jayaraman P, Bergseng E, Madhusudhan MS, Kim CY, Sollid LM
J Biol Chem 292 9218-9228 (2017)
PMID: 28364043

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135366 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class II histocompatibility antigen, DQ alpha 1 chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 199 amino acids
Theoretical weight: 22.42 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P01909 (Residues: 24-216; Coverage: 84%)
Gene name: HLA-DQA1
Sequence domains:
Structure domains:
Ig-like domain-containing protein Chains: B, E
Molecule details ›
Chains: B, E
Length: 204 amino acids
Theoretical weight: 23.78 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: Q5Y7D3 (Residues: 33-230; Coverage: 87%)
Gene name: HLA-DQB1
Sequence domains:
Structure domains:
Class-II-associated invariant chain peptide Chains: C, F
Molecule details ›
Chains: C, F
Length: 15 amino acids
Theoretical weight: 1.68 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P04233 (Residues: 103-117; Coverage: 5%)
Gene names: CD74, DHLAG

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C2
Unit cell:
a: 128.86Å b: 69.21Å c: 146.69Å
α: 90° β: 110.29° γ: 90°
R-values:
R R work R free
0.193 0.19 0.249
Expression system: unidentified baculovirus

Quick links

Citations

4 review citations

Class II MHC antigen processing in immune tolerance and inflammation.
Jurewicz et al. (2019)
3 more

2 mentions without citation

Unraveling the structural basis for the unusually rich association of human leukocyte antigen DQ2.5 with class-II-associated invariant chain peptides.
Nguyen et al. (2017)
1 more