SMTL ID : 8ve8.1

Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody (GP1-A epitope)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

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

NAG-NAG.1: 9 residues within 4Å: Chain A: E.76, T.77, N.79, M.80, N.99, W.227 Chain D: W.24, N.60, I.64 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: K.88, N.89, N.90, S.91, H.92, E.104 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: S.111, N.114, K.116, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: G.159, K.161, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: G.159, K.161, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain B: E.76, T.77, N.79, M.80, W.227 Chain E: W.24, I.64 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.64 NAG-NAG.11: 7 residues within 4Å: Chain B: I.113, K.116, Q.165, N.167, S.169, Y.219 Chain G: X.95 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain C: E.76, T.77, N.79, M.80, W.227 Chain F: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: K.88, N.89, S.91, H.92, E.104 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: G.159, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP)

5 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.3: 4 residues within 4Å: Chain A: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.6: 7 residues within 4Å: Chain B: N.109, S.216, Y.217, Q.218 Chain G: X.28, X.30 Chain H: X.102 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.10: 5 residues within 4Å: Chain B: H.115, F.117, N.119, D.156, N.158 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.117 NAG-NAG-FUC.14: 4 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.19: 2 residues within 4Å: Chain E: N.136, H.139 No protein-ligand interaction detected (PLIP)

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.9: 8 residues within 4Å: Chain B: K.88, N.89, N.90, H.92, Y.94, E.104 Chain G: X.56 Chain H: X.30 No protein-ligand interaction detected (PLIP)

1 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.15: 7 residues within 4Å: Chain C: S.111, I.113, K.116, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP)

3 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.17: 13 residues within 4Å: Chain A: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain D: N.106, S.108, V.129, G.132, Y.134 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Y.134 Hydrogen bonds: A:Q.232, A:D.229, A:Q.232 NAG-NAG-BMA-MAN.18: 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 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:Y.134 Hydrogen bonds: B:Q.232, B:D.229, B:Q.232 NAG-NAG-BMA-MAN.20: 14 residues within 4Å: Chain C: G.197, D.229, H.230, C.231, Q.232, F.233, S.234, R.235, S.237 Chain F: N.106, S.108, V.129, G.132, Y.134 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: F:Y.134 Hydrogen bonds: C:Q.232, C:D.229, C:Q.232

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

NAG.21: 2 residues within 4Å: Chain A: N.99, E.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.99, A:E.100 NAG.22: 5 residues within 4Å: Chain A: H.115, F.117, N.119, C.155, D.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.119, A:D.156 NAG.23: 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.24: 6 residues within 4Å: Chain C: H.115, F.117, N.119, C.155, D.156, N.158 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.119, C:N.158 NAG.25: 2 residues within 4Å: Chain C: N.99, E.100 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.100 Hydrogen bonds: C:N.99, C:E.100 NAG.26: 7 residues within 4Å: Chain A: Q.69 Chain D: K.32, C.33, F.34, Y.112, N.114, T.121 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.34, D:Y.112 Hydrogen bonds: D:K.32, D:Y.112 NAG.27: 1 residues within 4Å: Chain D: N.131 No protein-ligand interaction detected (PLIP) NAG.28: 3 residues within 4Å: Chain D: S.133, N.136, H.139 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.136 NAG.29: 7 residues within 4Å: Chain B: Q.69 Chain E: K.32, C.33, F.34, Y.112, N.114, T.121 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.34, E:Y.112, E:T.121 Hydrogen bonds: E:Y.112, E:N.114 NAG.30: 1 residues within 4Å: Chain E: N.131 No protein-ligand interaction detected (PLIP) NAG.31: 6 residues within 4Å: Chain C: Q.69 Chain F: K.32, C.33, Y.112, N.114, T.121 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:Y.112, F:T.121 Hydrogen bonds: F:Y.112, F:N.114 NAG.32: 2 residues within 4Å: Chain C: S.205 Chain F: N.131 No protein-ligand interaction detected (PLIP) 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

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
Rabbit polyclonal Fv light chain: G
Rabbit polyclonal Fv heavy chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
a

E
b

F
c

G
L

H
H

Glycoprotein G1

Glycoprotein G2

Rabbit polyclonal Fv light chain

Rabbit polyclonal Fv heavy chain

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