SMTL ID : 7sgd.1

Lassa virus glycoprotein construct(Josiah GPCysR4) recovered from GPC-I53-50 nanoparticle by localized reconstruction

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

18 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.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: G.160, K.161, N.224, T.225, T.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.160, A:K.161 NAG-NAG.4: 3 residues within 4Å: Chain A: N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: H.115, F.117, N.119, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain A: Q.69 Chain B: K.291, C.292, F.293, Y.371, N.373, T.380 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain C: G.160, K.161, N.224, T.225, T.226 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.160, C:K.161 NAG-NAG.13: 3 residues within 4Å: Chain C: N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: H.115, F.117, N.119, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 7 residues within 4Å: Chain C: Q.69 Chain D: K.291, C.292, F.293, Y.371, N.373, T.380 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain E: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain E: G.160, K.161, N.224, T.225, T.226 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.160, E:K.161 NAG-NAG.22: 3 residues within 4Å: Chain E: N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain E: H.115, F.117, N.119, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 7 residues within 4Å: Chain E: Q.69 Chain F: K.291, C.292, F.293, Y.371, N.373, T.380 No protein-ligand interaction detected (PLIP)

3 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: 8 residues within 4Å: Chain A: E.76, T.77, N.79, M.80, N.99, W.227 Chain B: W.283, I.323 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 8 residues within 4Å: Chain C: E.76, T.77, N.79, M.80, N.99, W.227 Chain D: W.283, I.323 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 8 residues within 4Å: Chain E: E.76, T.77, N.79, M.80, N.99, W.227 Chain F: W.283, I.323 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.7: 12 residues within 4Å: Chain A: M.75, D.229, C.231, F.233, S.234, R.235 Chain B: N.365, S.367, V.388, G.391, S.392, Y.393 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.233, A:R.235, A:D.229, A:C.231 NAG-NAG-BMA-MAN-MAN.16: 12 residues within 4Å: Chain C: M.75, D.229, C.231, F.233, S.234, R.235 Chain D: N.365, S.367, V.388, G.391, S.392, Y.393 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.233, C:R.235, C:D.229, C:C.231 NAG-NAG-BMA-MAN-MAN.25: 12 residues within 4Å: Chain E: M.75, D.229, C.231, F.233, S.234, R.235 Chain F: N.365, S.367, V.388, G.391, S.392, Y.393 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:F.233, E:R.235, E:D.229, E:C.231

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.9: 2 residues within 4Å: Chain B: N.395, H.398 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.18: 2 residues within 4Å: Chain D: N.395, H.398 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.27: 2 residues within 4Å: Chain F: N.395, H.398 No protein-ligand interaction detected (PLIP)

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

NAG.28: 4 residues within 4Å: Chain A: S.111, Q.165, N.167, Y.219 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.219 Hydrogen bonds: A:Y.219 NAG.29: 2 residues within 4Å: Chain A: Y.200 Chain B: N.390 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.200 NAG.30: 4 residues within 4Å: Chain C: S.111, Q.165, N.167, Y.219 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.219 Hydrogen bonds: C:Y.219 NAG.31: 2 residues within 4Å: Chain C: Y.200 Chain D: N.390 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.200 NAG.32: 4 residues within 4Å: Chain E: S.111, Q.165, N.167, Y.219 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.219 Hydrogen bonds: E:Y.219 NAG.33: 2 residues within 4Å: Chain E: Y.200 Chain F: N.390 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brouwer, P.J.M. et al., Lassa virus glycoprotein nanoparticles elicit neutralizing antibody responses and protection. Cell Host Microbe (2022)

Release Date

2022-10-12

Peptides

Josiah GPCysR4 I53-50A: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
a

C
B

D
b

E
C

F
c

Josiah GPCysR4 I53-50A

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