SMTL ID : 9cj7.1

Lineage IV Lassa virus glycoprotein (Josiah) in complex with monoclonal antibody 8.9F

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

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

NAG-NAG-BMA-MAN-MAN-FUC.1: 14 residues within 4Å: Chain A: H.115, F.117, N.119, D.122, K.126, N.158 Chain G: Y.144 Chain H: N.54, F.55, E.73, V.74, S.75, S.76, K.89 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain A Hydrogen bonds: H:S.75, H:S.76, A:D.156, H:F.55, A:K.126 Hydrophobic interactions: A:F.117, H:F.55, A:N.158 NAG-NAG-BMA-MAN-MAN-FUC.8: 10 residues within 4Å: Chain B: H.115, F.117, N.119, D.122 Chain G: S.76, S.78, T.95, D.126, D.127, Y.130 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.76, G:S.76, G:T.95, G:T.95, G:S.96, G:S.76

4 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.2: 7 residues within 4Å: Chain A: E.76, T.77, N.79, M.80, W.227 Chain D: W.24, I.64 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.24 Hydrophobic interactions: D:I.64 NAG-NAG-BMA.6: 8 residues within 4Å: Chain A: S.111, I.113, Q.165, N.167, S.169, H.170, Y.172, Y.219 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.172 Hydrogen bonds: A:Y.172, A:Y.172 NAG-NAG-BMA.9: 6 residues within 4Å: Chain B: E.76, T.77, N.79, M.80, W.227 Chain E: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 7 residues within 4Å: Chain C: E.76, T.77, N.79, M.80, W.227 Chain F: W.24, I.64 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.23, F:W.24 Hydrophobic interactions: F:I.64

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

NAG-NAG.3: 5 residues within 4Å: Chain A: K.88, N.89, N.90, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: M.80, N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: G.159, K.161, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 8 residues within 4Å: Chain B: S.111, N.114, K.116, Q.165, N.167, S.169, H.170, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain B: G.159, G.160, K.161, N.224, T.225, T.226 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.159 NAG-NAG.16: 5 residues within 4Å: Chain C: K.88, N.89, N.90, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: M.80, N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 8 residues within 4Å: Chain C: S.111, I.113, N.114, K.116, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain C: G.159, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 7 residues within 4Å: Chain A: Q.69 Chain D: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 8 residues within 4Å: Chain B: Q.69 Chain E: K.32, C.33, F.34, Y.112, N.114, T.116, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 9 residues within 4Å: Chain C: Q.69 Chain F: E.30, K.32, C.33, F.34, Y.112, N.114, T.116, T.121 No protein-ligand interaction detected (PLIP)

1 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.5: 4 residues within 4Å: Chain A: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-FUC.18: 3 residues within 4Å: Chain C: N.109, S.216, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.21: 3 residues within 4Å: Chain C: F.117, N.119, D.156 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.117

3 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.22: 14 residues within 4Å: Chain A: G.197, D.229, H.230, C.231, Q.232, F.233, S.234, R.235, S.237 Chain D: N.106, S.108, V.129, G.132, Y.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.232, A:R.235 NAG-NAG-BMA-MAN-MAN-MAN.24: 13 residues within 4Å: Chain B: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain E: N.106, S.108, V.129, G.132, Y.134 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Q.232 Hydrophobic interactions: E:Y.134 NAG-NAG-BMA-MAN-MAN-MAN.26: 14 residues within 4Å: Chain C: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain F: N.106, S.108, V.129, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.232

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.28: 1 residues within 4Å: Chain D: N.136 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.136 NAG.29: 3 residues within 4Å: Chain A: Y.200 Chain D: N.131, G.132 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.200 NAG.30: 2 residues within 4Å: Chain E: N.136, H.139 No protein-ligand interaction detected (PLIP) NAG.31: 1 residues within 4Å: Chain E: N.131 No protein-ligand interaction detected (PLIP) NAG.32: 1 residues within 4Å: Chain F: N.131 No protein-ligand interaction detected (PLIP) NAG.33: 2 residues within 4Å: Chain F: N.136, H.139 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brouwer, P.J.M. et al., Defining bottlenecks and opportunities for Lassa virus neutralization by structural profiling of vaccine-induced polyclonal antibody responses. Cell Rep (2024)

Release Date

2024-09-25

Peptides

Glycoprotein G1: ABC
Glycoprotein G2: DEF
Fv region of 8.9F heavy chain: G
Fv region of 8.9F light chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
c

E
a

F
b

G
H

H
L

Glycoprotein G1

Glycoprotein G2

Fv region of 8.9F heavy chain

Fv region of 8.9F light chain

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