SMTL ID : 9j03.1

Cyro-EM Structure of Human TLR4/MD-2/DLAM1 Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: N.8, S.13 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: N.8, S.13 No protein-ligand interaction detected (PLIP)

2 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.3: 6 residues within 4Å: Chain C: S.478, N.500, V.522, D.524 Ligands: NAG-NAG-NAG.5, NAG-NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 6 residues within 4Å: Chain D: S.478, N.500, V.522, D.524 Ligands: NAG-NAG-NAG.6, NAG-NAG-NAG.6 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-NAG.5: 6 residues within 4Å: Chain C: V.522, F.547, N.549, V.576 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.6: 6 residues within 4Å: Chain D: V.522, F.547, N.549, V.576 Ligands: NAG-NAG-BMA.4, NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP)

6 x 2IL: (3R)-3-(dodecanoyloxy)tetradecanoic acid(Non-covalent)

2IL.7: 12 residues within 4Å: Chain A: I.14, V.30, I.34, E.74, F.101, S.102, F.133, I.135 Ligands: 2IL.8, 2IL.9, GP4.18, X6Z.19 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.14, A:V.30, A:I.34, A:F.101, A:F.133, A:I.135 2IL.8: 10 residues within 4Å: Chain A: I.28, L.43, I.45, Y.84, I.99, F.101, S.102, F.133 Ligands: 2IL.7, GP4.18 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.28, A:L.43, A:I.45, A:I.45, A:I.99, A:F.101, A:F.133 Hydrogen bonds: A:S.102 2IL.9: 12 residues within 4Å: Chain A: I.34, L.36, I.62, F.103, K.104, I.106, F.108 Chain C: S.389, Q.410, E.413 Ligands: 2IL.7, X6Z.19 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.34, A:L.36, A:I.62, A:F.103, A:I.106, A:F.108 2IL.12: 12 residues within 4Å: Chain B: I.14, V.30, I.34, E.74, F.101, S.102, F.133, I.135 Ligands: 2IL.13, GP4.14, X6Z.15, 2IL.20 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.14, B:V.30, B:I.34, B:F.101, B:F.133, B:I.135 2IL.13: 10 residues within 4Å: Chain B: I.28, L.43, I.45, Y.84, I.99, F.101, S.102, F.133 Ligands: 2IL.12, GP4.14 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.28, B:L.43, B:I.45, B:I.45, B:I.99, B:F.101, B:F.133 Hydrogen bonds: B:S.102 2IL.20: 12 residues within 4Å: Chain B: I.34, L.36, I.62, F.103, K.104, I.106, F.108 Chain D: S.389, Q.410, E.413 Ligands: 2IL.12, X6Z.15 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.34, B:L.36, B:I.62, B:F.103, B:I.106, B:F.108

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

NAG.10: 2 residues within 4Å: Chain A: F.46, N.96 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.46 Hydrogen bonds: A:N.96 NAG.11: 2 residues within 4Å: Chain B: F.46, N.96 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.46 Hydrogen bonds: B:N.96 NAG.16: 2 residues within 4Å: Chain C: E.152, N.179 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.152 NAG.17: 2 residues within 4Å: Chain C: S.445, N.471 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain D: E.152, N.179 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.152 NAG.22: 2 residues within 4Å: Chain D: S.445, N.471 No protein-ligand interaction detected (PLIP)

2 x GP4: 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose(Non-covalent)

GP4.14: 5 residues within 4Å: Chain B: S.100 Chain C: R.238 Ligands: 2IL.12, 2IL.13, X6Z.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.238 GP4.18: 5 residues within 4Å: Chain A: S.100 Chain D: R.238 Ligands: 2IL.7, 2IL.8, X6Z.19 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.238

2 x X6Z: [(2~{R},3~{S},4~{S},5~{S})-5-methoxy-3,4,6-tris(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate(Non-covalent)

X6Z.15: 4 residues within 4Å: Chain C: K.336 Ligands: 2IL.12, GP4.14, 2IL.20 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.315, C:K.336 X6Z.19: 4 residues within 4Å: Chain D: K.336 Ligands: 2IL.7, 2IL.9, GP4.18 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.315, D:K.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fu, Y. et al., Structural insight into TLR4/MD-2 activation by synthetic LPS mimetics with distinct binding modes. Nat Commun (2025)

Release Date

2025-05-14

Peptides

Lymphocyte antigen 96: AB
Toll-like receptor 4: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
B

D
A

Lymphocyte antigen 96

Toll-like receptor 4

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