› 5y3l

X-ray diffraction
2.6Å resolution

Crystal structure of horse TLR9 in complex with two DNAs (CpG DNA and CCGCAC DNA)

Released:
DOI: 10.2210/pdb5y3l/pdb
PDB entry 5y3l coloured by chain, front view.
PDB entry 5y3l coloured by chain, side view.
PDB entry 5y3l coloured by chain, top view.
Source organisms:
Primary publication:
Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation.
Ohto U, Ishida H, Shibata T, Sato R, Miyake K, Shimizu T
Immunity 48 649-658.e4 (2018)
PMID: 29625894

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119424 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (4 distinct):
Toll-like receptor 9 Chains: A, B
Molecule details ›
Chains: A, B
Length: 802 amino acids
Theoretical weight: 89.43 KDa
Source organism: Equus caballus
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q2EEY0 (Residues: 26-819; Coverage: 79%)
Gene name: TLR9
Sequence domains:
Structure domains: Ribonuclease Inhibitor
DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 10 nucleotides
Theoretical weight: 3.07 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*CP*GP*CP*AP*C)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 6 nucleotides
Theoretical weight: 1.75 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 16 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 108.004Å b: 125.617Å c: 138.722Å
α: 90° β: 94.67° γ: 90°
R-values:
R R work R free
0.214 0.212 0.259
Expression systems:
  • Drosophila melanogaster
  • Not provided

Quick links

Citations

28 review citations

Toll-like Receptors and the Control of Immunity.
Fitzgerald et al. (2020)
27 more

3 mentions without citation

Structural and functional understanding of the toll-like receptors.
Asami et al. (2021)
2 more