SMTL ID : 6wxb.1

Cryo-EM Structure of Influenza Hemagglutinin (HA) Trimer Vitrified Using Back-it-up

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: S.45, S.46, N.285, V.297, N.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.285, A:V.297 NAG.2: 12 residues within 4Å: Chain A: N.165, V.166, T.167, V.244, N.246 Chain C: T.187, S.219, R.220, P.221, W.222, S.227 Ligands: NAG.11 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.219, C:S.219, C:R.220, C:W.222, A:N.165, A:T.167 NAG.3: 6 residues within 4Å: Chain A: Q.80, N.81, E.119, F.120, I.121, R.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.119, A:F.120 NAG.4: 8 residues within 4Å: Chain A: P.221, W.222 Chain B: T.167, R.207, V.242, V.244 Ligands: BMA.5, NAG.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.222 Hydrophobic interactions: B:V.242 NAG.6: 5 residues within 4Å: Chain B: S.45, S.46, N.285, V.297, N.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.285, B:V.297 NAG.7: 12 residues within 4Å: Chain A: T.187, S.219, R.220, P.221, W.222, S.227 Chain B: N.165, V.166, T.167, V.244, N.246 Ligands: NAG.4 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.219, A:S.219, A:R.220, A:W.222, B:N.165, B:T.167 NAG.8: 6 residues within 4Å: Chain B: Q.80, N.81, E.119, F.120, I.121, R.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.119, B:F.120 NAG.9: 8 residues within 4Å: Chain B: P.221, W.222 Chain C: T.167, R.207, V.242, V.244 Ligands: BMA.10, NAG.14 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.242 Hydrogen bonds: B:W.222 NAG.11: 8 residues within 4Å: Chain A: T.167, R.207, V.242, V.244 Chain C: P.221, W.222 Ligands: NAG.2, BMA.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.242 Hydrogen bonds: C:W.222 NAG.13: 5 residues within 4Å: Chain C: S.45, S.46, N.285, V.297, N.298 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.285, C:V.297 NAG.14: 12 residues within 4Å: Chain B: T.187, S.219, R.220, P.221, W.222, S.227 Chain C: N.165, V.166, T.167, V.244, N.246 Ligands: NAG.9 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.219, B:S.219, B:R.220, B:W.222, C:N.165, C:T.167 NAG.15: 6 residues within 4Å: Chain C: Q.80, N.81, E.119, F.120, I.121, R.150 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.119, C:F.120

3 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.5: 2 residues within 4Å: Chain A: W.222 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) BMA.10: 2 residues within 4Å: Chain B: W.222 Ligands: NAG.9 No protein-ligand interaction detected (PLIP) BMA.12: 2 residues within 4Å: Chain C: W.222 Ligands: NAG.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, Y.Z. et al., Through-grid wicking enables high-speed cryoEM specimen preparation. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-05-20

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hemagglutinin

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