› 5ts1

X-ray diffraction
2.3Å resolution

Crystal structure of MHC-I H2-KD complexed with peptides of Mycobacterial tuberculosis (YYQSGLSIV)

Released:
DOI: 10.2210/pdb5ts1/pdb
PDB entry 5ts1 coloured by chain, front view.
PDB entry 5ts1 coloured by chain, side view.
PDB entry 5ts1 coloured by chain, top view.
Source organisms:
Primary publication:
MHC-restricted Ag85B-specific CD8+ T cells are enhanced by recombinant BCG prime and DNA boost immunization in mice.
Komine-Aizawa S, Jiang J, Mizuno S, Hayakawa S, Matsuo K, Boyd LF, Margulies DH, Honda M
Eur J Immunol 49 1399-1414 (2019)
PMID: 31135967

Function and Biology Details

Reactions catalysed: 
2 alpha,alpha'-trehalose 6-mycolate = alpha,alpha'-trehalose + alpha,alpha'-trehalose 6,6'-bismycolate
Acyl-CoA + 1,2-diacylglycerol = CoA + triacylglycerol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135301 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, K-D alpha chain Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 275 amino acids
Theoretical weight: 32.16 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01902 (Residues: 23-297; Coverage: 79%)
Gene names: H2-K, H2-K1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
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
Diacylglycerol acyltransferase/mycolyltransferase Ag85B Chains: P, Q, R, S
Molecule details ›
Chains: P, Q, R, S
Length: 9 amino acids
Theoretical weight: 1.03 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Not provided
UniProt:
  • Canonical: P9WQP1 (Residues: 101-109; Coverage: 3%)
Gene names: MTCY180.32, Rv1886c, fbpB

Ligands and Environments

2 bound ligands:
Ligand GOL 6 x GOL
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P1
Unit cell:
a: 47.302Å b: 88.96Å c: 109.947Å
α: 89.97° β: 93.83° γ: 90.04°
R-values:
R R work R free
0.189 0.187 0.224
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

Fighting Tuberculosis: In Search of a BCG Replacement.
Nadolinskaia et al. (2022)
5 other articles

1 mention without citation

MHC-restricted Ag85B-specific CD8+ T cells are enhanced by recombinant BCG prime and DNA boost immunization in mice.
Komine-Aizawa et al. (2019)