› 6cqn

X-ray diffraction
2.5Å resolution

Crystal structure of F5 TCR -DR11-RQ13 peptide complex

Released:
DOI: 10.2210/pdb6cqn/pdb
PDB entry 6cqn coloured by chain, front view.
PDB entry 6cqn coloured by chain, side view.
PDB entry 6cqn coloured by chain, top view.
Source organisms:
Primary publication:
CD4+ T cell-mediated HLA class II cross-restriction in HIV controllers.
Galperin M, Farenc C, Mukhopadhyay M, Jayasinghe D, Decroos A, Benati D, Tan LL, Ciacchi L, Reid HH, Rossjohn J, Chakrabarti LA, Gras S
Sci Immunol 3 (2018)
PMID: 29884618

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-100930 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
HLA class II histocompatibility antigen, DR alpha chain Chain: A
Molecule details ›
Chain: A
Length: 182 amino acids
Theoretical weight: 21.19 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01903 (Residues: 26-207; Coverage: 80%)
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: 190 amino acids
Theoretical weight: 22.25 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01911 (Residues: 30-219; Coverage: 80%)
Gene name: HLA-DRB1
Sequence domains:
Structure domains:
Capsid protein p24 Chain: C
Molecule details ›
Chain: C
Length: 13 amino acids
Theoretical weight: 1.6 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Homo sapiens
UniProt:
  • Canonical: P04585 (Residues: 299-311; Coverage: 1%)
Gene name: gag-pol
T cell receptor alpha variable 24 Chain: D
Molecule details ›
Chain: D
Length: 205 amino acids
Theoretical weight: 22.8 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A0B4J272 (Residues: 23-114; Coverage: 100%)
Gene name: TRAV24
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chain: E
Molecule details ›
Chain: E
Length: 245 amino acids
Theoretical weight: 27.98 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A0G2JMB4 (Residues: 2-130; Coverage: 72%)
Gene name: TRBC2
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

4 bound ligands:
Ligand NAG 2 x NAG
Ligand SO4 4 x SO4
Ligand CL 2 x CL
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P21212
Unit cell:
a: 75.317Å b: 205.792Å c: 70.229Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.196 0.251
Expression system: Homo sapiens

Quick links

Citations

7 review citations

The Many Faces of CD4+ T Cells: Immunological and Structural Characteristics.
Chatzileontiadou et al. (2020)
6 more

1 mention without citation

Genome-wide pharmacogenetics of anti-drug antibody response to bococizumab highlights key residues in HLA DRB1 and DQB1.
Chasman et al. (2022)