› 5wer

X-ray diffraction
3.41Å resolution

Crystal Structure of TAPBPR and H2-Dd complex

Released:
DOI: 10.2210/pdb5wer/pdb
PDB entry 5wer coloured by chain, front view.
PDB entry 5wer coloured by chain, side view.
PDB entry 5wer coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of a TAPBPR-MHC I complex reveals the mechanism of peptide editing in antigen presentation.
Jiang J, Natarajan K, Boyd LF, Morozov GI, Mage MG, Margulies DH
Science 358 1064-1068 (2017)
PMID: 29025991

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-135293 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, D-D alpha chain Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 277 amino acids
Theoretical weight: 32.28 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01900 (Residues: 26-301; Coverage: 81%)
Gene name: H2-D1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Tapasin-related protein Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 394 amino acids
Theoretical weight: 42.28 KDa
Source organism: Homo sapiens
Expression system: Drosophila acanthoptera
UniProt:
  • Canonical: Q9BX59 (Residues: 22-410; Coverage: 86%)
Gene name: TAPBPL
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand EDO 2 x EDO
Ligand GOL 3 x GOL
Ligand 1PE 1 x 1PE
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID, APS BEAMLINE 23-ID-B
Spacegroup: P31
Unit cell:
a: 169.05Å b: 169.05Å c: 139.41Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.243 0.239 0.269
Expression systems:
  • Escherichia coli BL21(DE3)
  • Drosophila acanthoptera

Quick links

Citations

8 review citations

Polymorphisms of HLA-B: influences on assembly and immunity.
Olson et al. (2020)
7 more

17 mentions without citation

The mode of action of tapasin on major histocompatibility class I (MHC-I) molecules.
Lan et al. (2023)
16 more