SMTL ID : 8ejd.1

Structure of lineage IV Lassa virus glycoprotein complex (strain Josiah)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

6 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: 9 residues within 4Å: Chain A: E.76, T.77, N.79, M.80, N.99, W.227 Chain B: R.23, W.24, I.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.23 Hydrophobic interactions: A:T.77, B:W.24 NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 9 residues within 4Å: Chain C: E.76, T.77, N.79, M.80, N.99, W.227 Chain D: R.23, W.24, I.64 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.23 Hydrophobic interactions: C:T.77, D:W.24 NAG-NAG-BMA.11: 4 residues within 4Å: Chain C: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 9 residues within 4Å: Chain E: E.76, T.77, N.79, M.80, N.99, W.227 Chain F: R.23, W.24, I.64 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.23 Hydrophobic interactions: E:T.77, F:W.24 NAG-NAG-BMA.20: 4 residues within 4Å: Chain E: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 2 residues within 4Å: Chain A: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: H.115, F.117, N.119, C.155, D.156 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 10 residues within 4Å: Chain A: I.113, N.114, Q.165, N.167, S.169, H.170, Y.172, A.173, G.174, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: G.160, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain C: H.115, F.117, N.119, C.155, D.156 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 10 residues within 4Å: Chain C: I.113, N.114, Q.165, N.167, S.169, H.170, Y.172, A.173, G.174, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: G.160, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain E: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain E: H.115, F.117, N.119, C.155, D.156 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 10 residues within 4Å: Chain E: I.113, N.114, Q.165, N.167, S.169, H.170, Y.172, A.173, G.174, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain E: G.160, N.224 No protein-ligand interaction detected (PLIP)

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.4: 4 residues within 4Å: Chain A: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.13: 4 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.22: 4 residues within 4Å: Chain E: N.109, S.216, Y.217, Q.218 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.8: 10 residues within 4Å: Chain A: C.231, Q.232, F.233, S.234, R.235 Chain B: N.106, S.108, V.129, G.132, Y.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.233, A:S.234, A:R.235 NAG-NAG-BMA-MAN-MAN.17: 10 residues within 4Å: Chain C: C.231, Q.232, F.233, S.234, R.235 Chain D: N.106, S.108, V.129, G.132, Y.134 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.233, C:S.234, C:R.235 NAG-NAG-BMA-MAN-MAN.26: 10 residues within 4Å: Chain E: C.231, Q.232, F.233, S.234, R.235 Chain F: N.106, S.108, V.129, G.132, Y.134 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:F.233, E:S.234, E:R.235

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-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.9: 9 residues within 4Å: Chain A: Q.69 Chain B: R.23, E.30, K.32, C.33, F.34, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.30 NAG-NAG-BMA-MAN-MAN.18: 9 residues within 4Å: Chain C: Q.69 Chain D: R.23, E.30, K.32, C.33, F.34, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.30 NAG-NAG-BMA-MAN-MAN.27: 9 residues within 4Å: Chain E: Q.69 Chain F: R.23, E.30, K.32, C.33, F.34, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.30

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

NAG.28: 1 residues within 4Å: Chain B: N.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.131 NAG.29: 1 residues within 4Å: Chain B: N.136 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.136 NAG.30: 1 residues within 4Å: Chain D: N.131 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.131 NAG.31: 1 residues within 4Å: Chain D: N.136 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.136 NAG.32: 1 residues within 4Å: Chain F: N.131 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.131 NAG.33: 1 residues within 4Å: Chain F: N.136 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perrett, H.R. et al., Structural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies. Cell Rep (2023)

Release Date

2023-06-07

Peptides

Glycoprotein G1: ACE
Glycoprotein G2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

E
B

B
c

D
a

F
b

Glycoprotein G1

Glycoprotein G2

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