SMTL ID : 7tyv.1

Structure of Lassa Virus glycoprotein (Josiah) bound to Fab 25.10C

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 12 residues within 4Å: Chain A: E.76, T.77, N.79, M.80 Chain D: R.101, R.102, A.103, S.104 Chain E: V.73, N.74 Chain J: W.24, N.60 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.74 NAG-NAG-BMA-MAN-MAN.5: 10 residues within 4Å: Chain B: E.76, T.77, N.79, M.80 Chain F: R.101, R.102, A.103, S.104 Chain I: V.73, N.74 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.74 NAG-NAG-BMA-MAN-MAN.9: 10 residues within 4Å: Chain C: E.76, T.77, N.79, M.80 Chain G: V.73, N.74 Chain H: R.101, R.102, A.103, S.104 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.74

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

NAG-NAG.2: 8 residues within 4Å: Chain A: M.80, N.99, E.100 Chain D: K.31, Y.32, R.98, I.100, D.109 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.109, D:D.109 NAG-NAG.3: 8 residues within 4Å: Chain A: G.159, G.160, K.161, N.224, T.225, T.226 Chain D: N.30, K.31 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.30, D:K.31 NAG-NAG.6: 5 residues within 4Å: Chain B: N.99, E.100 Chain F: K.31, Y.32, I.100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain B: G.159, G.160, N.224, T.225, T.226 Chain F: N.30, K.31 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.30, F:K.31, F:K.31 NAG-NAG.10: 6 residues within 4Å: Chain C: N.99, E.100 Chain H: K.31, Y.32, I.100, D.109 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:D.109, H:D.109

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.4: 14 residues within 4Å: Chain A: D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain D: Y.59 Chain E: D.113 Chain J: N.106, S.108, V.129, G.132, Y.134 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.232, D:Y.59

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.8: 14 residues within 4Å: Chain B: D.229, C.231, Q.232, F.233, S.234, R.235 Chain F: Y.59 Chain I: D.113, T.114 Chain K: N.106, S.108, V.129, S.133, Y.134 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain I Hydrogen bonds: B:Q.232, I:D.113, B:C.231 NAG-NAG-BMA-MAN-MAN-MAN.12: 14 residues within 4Å: Chain C: D.229, C.231, Q.232, F.233, S.234, R.235 Chain G: D.113, T.114 Chain H: Y.57, Y.59 Chain L: N.106, S.108, G.132, Y.134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.232

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.11: 7 residues within 4Å: Chain C: G.159, G.160, K.161, N.224, T.225, T.226 Chain H: N.30 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain H Hydrogen bonds: C:G.159, H:N.30

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

NAG.13: 4 residues within 4Å: Chain A: K.88, N.89, S.91, Y.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.88, A:N.89 NAG.14: 3 residues within 4Å: Chain A: N.109, S.216, Y.217 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.217 Hydrogen bonds: A:N.109, A:S.216 NAG.15: 8 residues within 4Å: Chain A: I.113, N.114, H.115, K.116, S.154, Q.165, N.167, Y.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.114, A:N.167 NAG.16: 3 residues within 4Å: Chain B: K.88, N.89, S.91 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.88, B:K.88, B:N.89 NAG.17: 3 residues within 4Å: Chain B: N.109, S.216, Y.217 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.217 NAG.18: 9 residues within 4Å: Chain B: I.113, N.114, H.115, K.116, S.154, Q.165, N.167, S.169, Y.219 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.114, B:S.154, B:N.167, B:Y.219 NAG.19: 4 residues within 4Å: Chain C: K.88, N.89, S.91, Y.217 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.89 NAG.20: 3 residues within 4Å: Chain C: N.109, S.216, Q.218 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.216, C:Q.218 NAG.21: 6 residues within 4Å: Chain C: N.114, H.115, K.116, S.154, N.167, Y.219 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.116 Hydrogen bonds: C:N.114, C:S.154 NAG.22: 8 residues within 4Å: Chain A: Q.69 Chain J: K.32, C.33, F.34, Y.112, N.114, T.116, T.121 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:F.34, J:Y.112, J:T.121 Hydrogen bonds: J:N.114 NAG.23: 1 residues within 4Å: Chain J: N.136 No protein-ligand interaction detected (PLIP) NAG.24: 6 residues within 4Å: Chain K: K.32, C.33, F.34, Y.112, N.114, T.121 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:F.34, K:Y.112, K:T.121 NAG.25: 5 residues within 4Å: Chain L: C.33, F.34, Y.112, N.114, T.121 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:F.34, L:Y.112, L:T.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Enriquez, A.S. et al., Delineating the mechanism of anti-Lassa virus GPC-A neutralizing antibodies. Cell Rep (2022)

Release Date

2022-06-01

Peptides

Glycoprotein G1: ABC
25.10C Fab Heavy Chain: DFH
25.10C Fab Light Chain: EGI
Glycoprotein G2: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
G

H
H

E
E

G
L

I
K

J
a

K
b

L
c

Glycoprotein G1

25.10C Fab Heavy Chain

25.10C Fab Light Chain

Glycoprotein G2

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