SMTL ID : 8eji.1

Lassa virus glycoprotein complex (Josiah) bound to 19.7E Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-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 Ligands: NAG-NAG-BMA.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.23, B:R.23 NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: N.99 Ligands: NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 6 residues within 4Å: Chain A: G.159, G.160, K.161, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 6 residues within 4Å: Chain A: Q.69 Chain B: K.32, C.33, F.34, Y.112, N.114 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: W.24, I.64 Ligands: NAG.23 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.24 NAG-NAG-BMA.15: 9 residues within 4Å: Chain G: E.76, T.77, N.79, M.80, N.99, W.227 Chain H: W.24, I.64 Ligands: NAG.29 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:W.24

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-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.2: 9 residues within 4Å: Chain A: K.88, N.89, N.90, S.91, H.92 Chain E: E.1, W.109 Chain F: A.43, K.45 No protein-ligand interaction detected (PLIP)

2 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.4: 5 residues within 4Å: Chain A: N.109, Y.172, S.216, Y.217 Chain E: W.104 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.172 NAG-NAG-BMA-MAN-MAN.8: 16 residues within 4Å: Chain A: M.75, G.197, Y.200, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain B: N.106, S.108, V.129, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.232, A:R.235

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

NAG-NAG.5: 4 residues within 4Å: Chain A: H.115, F.117, N.119, C.155 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain C: S.111, I.113, N.114, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain C: L.128, D.130, G.159, G.160, K.161, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain C: E.67, Q.69 Chain D: L.31, K.32, Y.112, N.114, H.115, T.116 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:K.32 NAG-NAG.16: 7 residues within 4Å: Chain G: S.111, I.113, N.114, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain G: L.128, D.130, G.159, G.160, K.161, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 8 residues within 4Å: Chain G: E.67, Q.69 Chain H: L.31, K.32, Y.112, N.114, H.115, T.116 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:K.32

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-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.6: 7 residues within 4Å: Chain A: I.113, Q.165, N.167, S.169, Y.219 Chain E: Y.102 Chain F: N.92 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.92

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.13: 10 residues within 4Å: Chain C: C.231, Q.232, F.233, S.234, R.235 Chain D: N.106, S.108, V.129, S.133, Y.134 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.232, C:R.235 Hydrophobic interactions: D:Y.134 NAG-NAG-BMA-MAN-MAN-MAN.18: 11 residues within 4Å: Chain G: C.231, Q.232, F.233, S.234, R.235 Chain H: N.106, S.108, V.129, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.232, G:R.235

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

NAG.20: 3 residues within 4Å: Chain A: C.207 Chain B: C.101, N.131 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain B: Y.134, N.136 No protein-ligand interaction detected (PLIP) NAG.22: 3 residues within 4Å: Chain C: N.89, S.91, H.92 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.92 NAG.23: 2 residues within 4Å: Chain C: N.99 Ligands: NAG-NAG-BMA.10 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.99 NAG.24: 3 residues within 4Å: Chain C: N.109, S.216, Y.217 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.217 Hydrogen bonds: C:S.216, C:Q.218 NAG.25: 3 residues within 4Å: Chain C: H.115, F.117, N.119 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.117 Hydrogen bonds: C:N.119 NAG.26: 4 residues within 4Å: Chain C: Y.200, C.207 Chain D: C.101, N.131 No protein-ligand interaction detected (PLIP) NAG.27: 2 residues within 4Å: Chain D: N.136, H.139 No protein-ligand interaction detected (PLIP) NAG.28: 3 residues within 4Å: Chain G: N.89, S.91, H.92 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.92 NAG.29: 2 residues within 4Å: Chain G: N.99 Ligands: NAG-NAG-BMA.15 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:N.99 NAG.30: 3 residues within 4Å: Chain G: N.109, S.216, Y.217 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:Y.217 Hydrogen bonds: G:S.216, G:Q.218 NAG.31: 3 residues within 4Å: Chain G: H.115, F.117, N.119 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.117 Hydrogen bonds: G:N.119 NAG.32: 4 residues within 4Å: Chain G: Y.200, C.207 Chain H: C.101, N.131 No protein-ligand interaction detected (PLIP) NAG.33: 2 residues within 4Å: Chain H: N.136, H.139 No protein-ligand interaction detected (PLIP)

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: ACG
Glycoprotein G2: BDH
19.7E Fab heavy chain: E
19.7E Fab light chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

G
C

B
a

D
b

H
c

E
H

F
L

Glycoprotein G1

Glycoprotein G2

19.7E Fab heavy chain

19.7E Fab light chain

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