› 5ijb

X-ray diffraction
2.91Å resolution

The ligand-free structure of the mouse TLR4/MD-2 complex

Released:
DOI: 10.2210/pdb5ijb/pdb
PDB entry 5ijb coloured by chain, front view.
PDB entry 5ijb coloured by chain, side view.
PDB entry 5ijb coloured by chain, top view.
Source organisms:
Primary publication:
TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS.
Wang Y, Su L, Morin MD, Jones BT, Whitby LR, Surakattula MM, Huang H, Shi H, Choi JH, Wang KW, Moresco EM, Berger M, Zhan X, Zhang H, Boger DL, Beutler B
Proc Natl Acad Sci U S A 113 E884-93 (2016)
PMID: 26831104

Function and Biology Details

Reaction catalysed: 
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175535 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
LRRNT domain-containing protein; Toll-like receptor 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 594 amino acids
Theoretical weight: 67.28 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9QUK6 (Residues: 26-544; Coverage: 64%)
  • Canonical: Q4G1L2 (Residues: 126-200; Coverage: 30%)
Gene names: Lps, Tlr4, VLRB
Sequence domains:
Structure domains: Ribonuclease Inhibitor
Lymphocyte antigen 96 Chains: C, D
Molecule details ›
Chains: C, D
Length: 150 amino acids
Theoretical weight: 17.39 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9JHF9 (Residues: 19-160; Coverage: 100%)
Gene names: Esop1, Ly96, Md2
Structure domains: Immunoglobulin-like

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 6 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P43212
Unit cell:
a: 128.32Å b: 128.32Å c: 277.507Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.246 0.243 0.308
Expression system: Spodoptera frugiperda

Quick links

Citations

27 review citations

Modulators of microglial activation and polarization after intracerebral haemorrhage.
Lan et al. (2017)
26 more

12 mentions without citation

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Dey et al. (2022)
11 more