SMTL ID : 8vcv.1

Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody (GPC-C epitope)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-3-mer

Ligands

1 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.1: 10 residues within 4Å: Chain A: C.118, N.119, D.122, K.126 Chain D: X.102, X.104, X.110 Chain E: X.47, X.48, X.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.122, A:K.126

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

NAG-NAG.2: 9 residues within 4Å: Chain A: S.111, N.114, K.116, Q.165, N.167, S.169, Y.219 Chain E: X.94, X.95 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 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.5: 7 residues within 4Å: Chain A: E.76, T.77, N.79, M.80, N.99, W.227 Chain F: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.109, S.216, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain B: E.76, T.77, N.79, M.80, N.99, W.227 Chain G: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain B: S.111, I.113, K.116, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain B: G.159, K.161, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain C: G.159, K.161, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain F: Y.134, N.136, H.139 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 7 residues within 4Å: Chain C: Q.69 Chain H: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain H: Y.134, N.136 No protein-ligand interaction detected (PLIP)

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.8: 7 residues within 4Å: Chain B: K.88, N.89, N.90, S.91, H.92, Y.94, E.104 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 7 residues within 4Å: Chain C: I.113, K.116, Q.165, N.167, S.169, Y.219 Ligands: NAG-NAG-FUC.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 9 residues within 4Å: Chain C: E.76, T.77, N.79, M.80, N.99, W.227 Chain H: W.24, N.60, I.64 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.64 NAG-NAG-BMA.16: 7 residues within 4Å: Chain C: K.88, N.89, N.90, S.91, H.92, Y.94, E.104 No protein-ligand interaction detected (PLIP)

4 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: 4 residues within 4Å: Chain B: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.10: 6 residues within 4Å: Chain B: H.115, F.117, N.119, C.155, D.156, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.14: 5 residues within 4Å: Chain C: H.115, F.117, N.119, D.156, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.17: 5 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 Ligands: NAG-NAG-BMA.13 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.19: 15 residues within 4Å: Chain A: G.197, D.229, H.230, C.231, Q.232, F.233, S.234, R.235, P.236, S.237 Chain F: N.106, S.108, V.129, G.132, Y.134 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:Q.232, A:C.231 Hydrophobic interactions: F:Y.134

1 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.21: 14 residues within 4Å: Chain B: G.197, D.229, H.230, C.231, Q.232, F.233, S.234, R.235, S.237 Chain G: N.106, S.108, V.129, G.132, Y.134 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:Q.232 Hydrophobic interactions: G:Y.134

1 x NAG- NAG- BMA- MAN: 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.22: 14 residues within 4Å: Chain C: M.75, G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain H: N.106, S.108, V.129, G.132, Y.134 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain H Hydrogen bonds: C:Q.232, C:D.229, C:Q.232 Hydrophobic interactions: H:Y.134

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

NAG.25: 1 residues within 4Å: Chain A: N.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.99 NAG.26: 2 residues within 4Å: Chain B: N.99, E.100 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.100 Hydrogen bonds: B:N.99, B:E.100, B:E.100 NAG.27: 3 residues within 4Å: Chain C: M.80, N.99, E.100 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.100 Hydrogen bonds: C:E.100 NAG.28: 7 residues within 4Å: Chain A: Q.69 Chain F: K.32, C.33, F.34, Y.112, N.114, T.121 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:F.34, F:Y.112, F:T.121 Hydrogen bonds: F:K.32, F:Y.112, F:N.114 NAG.29: 2 residues within 4Å: Chain A: C.207 Chain F: N.131 No protein-ligand interaction detected (PLIP) NAG.30: 6 residues within 4Å: Chain G: K.32, C.33, F.34, Y.112, N.114, T.121 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:F.34, G:Y.112, G:T.121 Hydrogen bonds: G:K.32, G:Y.112, G:N.114 NAG.31: 2 residues within 4Å: Chain G: N.136, H.139 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.136 NAG.32: 3 residues within 4Å: Chain B: G.206, C.207 Chain G: N.131 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.131 NAG.33: 3 residues within 4Å: Chain C: S.205, C.207 Chain H: N.131 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
Rabbit polyclonal Fv heavy chain: D
Rabbit polyclonal Fv light chain: E
Glycoprotein G2: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

F
a

G
b

H
c

Glycoprotein G1

Rabbit polyclonal Fv heavy chain

Rabbit polyclonal Fv light chain

Glycoprotein G2

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