SMTL ID : 7wm4.1

Cryo-EM structure of tetrameric TLR3 in complex with dsRNA (90 bp)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

14 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.223, W.249 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain A: N.374, E.375, W.405 Ligands: NAG-NAG-BMA.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain A: S.363, N.389, T.391, D.413 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain A: N.400, S.424, Q.426 Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain B: N.374, N.400, R.429 Ligands: NAG-NAG-BMA.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain B: N.389, D.413, Y.438 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain B: N.400, S.424, Q.426 Ligands: NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 3 residues within 4Å: Chain C: S.222, N.223, W.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 4 residues within 4Å: Chain C: N.374, E.375, W.405 Ligands: NAG-NAG-BMA.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 5 residues within 4Å: Chain C: S.363, N.389, T.391, K.392, D.413 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 5 residues within 4Å: Chain C: N.400, S.424, Q.426 Ligands: NAG-NAG-BMA.19, NAG-NAG-BMA.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 5 residues within 4Å: Chain D: N.374, N.400, W.405, R.429 Ligands: NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 4 residues within 4Å: Chain D: L.388, N.389, D.413, Y.438 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 4 residues within 4Å: Chain D: N.400, S.424, Q.426 Ligands: NAG-NAG-BMA.25 No protein-ligand interaction detected (PLIP)

14 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain A: R.176, Q.227, N.228, Q.254, Y.278 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.278 Hydrogen bonds: A:Q.254 NAG-NAG.3: 8 residues within 4Å: Chain A: K.248, W.249, T.250, N.251, P.274, S.275 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: N.267, S.290, P.291, R.292, D.323, D.324 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.291 Hydrogen bonds: A:D.323 NAG-NAG.8: 2 residues within 4Å: Chain A: S.457, N.483 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.223, W.249 Ligands: NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.228, Q.254, Y.278 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.278 Hydrogen bonds: B:Y.278 NAG-NAG.14: 2 residues within 4Å: Chain B: S.457, N.483 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: Q.227, N.228, Q.254, Y.278 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: K.248, T.250, N.251 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: N.267, P.291, R.292, D.323 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.291 NAG-NAG.22: 3 residues within 4Å: Chain C: P.456, S.457, N.483 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain D: S.222, N.223, W.249 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain D: R.176, N.228, Q.254, Y.278 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.278 Hydrogen bonds: D:Y.278 NAG-NAG.28: 2 residues within 4Å: Chain D: S.457, N.483 No protein-ligand interaction detected (PLIP)

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.29: 5 residues within 4Å: Chain A: H.20, I.21, R.41, P.43, N.46 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.43 Hydrogen bonds: A:I.21, A:N.46 NAG.30: 2 residues within 4Å: Chain A: E.147, N.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.172 NAG.31: 4 residues within 4Å: Chain B: I.21, R.41, P.43, N.46 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.21, B:P.43 Hydrogen bonds: B:I.21 NAG.32: 3 residues within 4Å: Chain B: V.144, E.147, N.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.147 NAG.33: 7 residues within 4Å: Chain B: N.223, T.224, S.225, W.249, T.250, N.251 Ligands: NAG-NAG.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.225, B:W.249, B:T.250, B:N.251 NAG.34: 3 residues within 4Å: Chain B: V.265, G.266, N.267 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.267 NAG.35: 4 residues within 4Å: Chain C: H.20, I.21, P.43, N.46 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:H.20, C:I.21 Hydrogen bonds: C:I.21, C:N.46 NAG.36: 3 residues within 4Å: Chain C: V.144, E.147, N.172 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.144, C:E.147 Hydrogen bonds: C:N.172 NAG.37: 5 residues within 4Å: Chain D: H.20, I.21, R.41, P.43, N.46 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.21, D:P.43 Hydrogen bonds: D:I.21 NAG.38: 3 residues within 4Å: Chain D: V.144, E.147, N.172 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.172 Hydrogen bonds: D:E.147 NAG.39: 5 residues within 4Å: Chain D: K.198, S.225, W.249, T.250, N.251 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:N.251 Hydrogen bonds: D:K.198, D:K.198, D:W.249 NAG.40: 3 residues within 4Å: Chain D: V.265, G.266, N.267 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakaniwa, K. et al., TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction. Nat Commun (2023)

Release Date

2023-01-25

Peptides

Toll-like receptor 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

Toll-like receptor 3