› 4gbx

X-ray diffraction
3Å resolution

Crystal structure of an immune complex at pH 6.5

Released:
DOI: 10.2210/pdb4gbx/pdb
PDB entry 4gbx coloured by chain, front view.
PDB entry 4gbx coloured by chain, side view.
PDB entry 4gbx coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of the HLA-DM-HLA-DR1 complex defines mechanisms for rapid peptide selection.
Pos W, Sethi DK, Call MJ, Schulze MS, Anders AK, Pyrdol J, Wucherpfennig KW
Cell 151 1557-68 (2012)
PMID: 23260142

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-219173 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
HLA class II histocompatibility antigen, DM alpha chain Chain: C
Molecule details ›
Chain: C
Length: 203 amino acids
Theoretical weight: 22.99 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P28067 (Residues: 27-225; Coverage: 85%)
Gene names: DMA, HLA-DMA, RING6
Sequence domains:
Structure domains:
HLA class II histocompatibility antigen, DM beta chain Chain: D
Molecule details ›
Chain: D
Length: 199 amino acids
Theoretical weight: 22.23 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P28068 (Residues: 19-211; Coverage: 79%)
Gene names: DMB, HLA-DMB, RING7
Sequence domains:
Structure domains:
HLA class II histocompatibility antigen, DR alpha chain Chain: A
Molecule details ›
Chain: A
Length: 191 amino acids
Theoretical weight: 22.11 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P01903 (Residues: 26-216; Coverage: 83%)
Gene names: HLA-DRA, HLA-DRA1
Sequence domains:
Structure domains:
HLA class II histocompatibility antigen, DRB1 beta chain Chain: B
Molecule details ›
Chain: B
Length: 208 amino acids
Theoretical weight: 23.74 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P01911 (Residues: 30-220; Coverage: 81%)
Gene name: HLA-DRB1
Sequence domains:
Structure domains:
synthetic peptide Chain: E
Molecule details ›
Chain: E
Length: 10 amino acids
Theoretical weight: 1.08 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NAG 3 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 66.167Å b: 126.032Å c: 143.107Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.25
Expression systems:
  • Cricetulus griseus
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

43 review citations

HLA-DM and HLA-DO, key regulators of MHC-II processing and presentation.
Mellins et al. (2014)
42 more

13 mentions without citation

Crystal structure of the HLA-DM-HLA-DR1 complex defines mechanisms for rapid peptide selection.
Pos et al. (2012)
12 more