› 6bj2

X-ray diffraction
3.35Å resolution

TCR589 in complex with HIV(Pol448-456)/HLA-B35

Released:
DOI: 10.2210/pdb6bj2/pdb
Model geometry
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PDB entry 6bj2 coloured by chain, front view.
PDB entry 6bj2 coloured by chain, side view.
PDB entry 6bj2 coloured by chain, top view.
Source organisms:
Primary publication:
Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding.
Sibener LV, Fernandes RA, Kolawole EM, Carbone CB, Liu F, McAffee D, Birnbaum ME, Yang X, Su LF, Yu W, Dong S, Gee MH, Jude KM, Davis MM, Groves JT, Goddard WA, Heath JR, Evavold BD, Vale RD, Garcia KC
Cell 174 672-687.e27 (2018)
PMID: 30053426

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-125600 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (6 distinct):
Ig-like domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 206 amino acids
Theoretical weight: 23.28 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6IRV4 (Residues: 22-123, 124-227; Coverage: 80%)
Gene name: TRA@
Sequence domains:
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chain: E
Molecule details ›
Chain: E
Length: 241 amino acids
Theoretical weight: 27.19 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: K7N5M4 (Residues: 5-249; Coverage: 93%)
Gene names: B2M, HDCMA22P
Sequence domains:
Structure domains: Immunoglobulins
HLA class I histocompatibility antigen, B alpha chain Chain: A
Beta-2-microglobulin Chain: B
p51 RT Chain: C

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand ZN 3 x ZN
Ligand NAG 1 x NAG
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C2
Unit cell:
a: 156.48Å b: 59.28Å c: 123.57Å
α: 90° β: 110.77° γ: 90°
R-values:
R R work R free
0.247 0.245 0.276
Expression systems:
  • Trichoplusia ni
  • Not provided

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Citations

61 review citations

The structural basis of T-cell receptor (TCR) activation: An enduring enigma.
Mariuzza et al. (2020)
60 more

2 mentions without citation

TCR Recognition of Peptide-MHC-I: Rule Makers and Breakers.
Szeto et al. (2020)
1 more

PDB-REDO

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