SMTL ID : 9ck8.1

Lineage IV Lassa virus glycoprotein (Josiah) in complex with polyclonal antibody (GPC-A epitope) from rabbit 189

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

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

NAG-NAG.1: 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.2: 9 residues within 4Å: Chain C: E.76, T.77, N.79, M.80, N.99, W.227 Chain H: W.24, I.64 Ligands: NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain D: M.80, N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain D: S.111, N.114, K.116, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain D: E.76, T.77, N.79, M.80, N.99 Chain F: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain E: K.88, N.89, N.90, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain E: I.113, K.116, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain E: N.158, G.159, G.160, K.161, N.224, T.226 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.161 Hydrogen bonds: E:G.159 NAG-NAG.13: 6 residues within 4Å: Chain F: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 13 residues within 4Å: Chain D: M.75, G.197, F.233, S.234, R.235, P.236, S.237 Chain F: N.106, S.108, V.129, G.132, S.133, Y.134 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 11 residues within 4Å: Chain C: G.197, F.233, S.234, R.235, S.237 Chain H: N.106, S.108, V.129, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:Y.134

3 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: 6 residues within 4Å: Chain C: H.115, F.117, N.119, C.155, D.156, N.158 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.115, C:D.156, C:N.158 NAG-NAG-FUC.7: 4 residues within 4Å: Chain D: H.115, F.117, N.119, D.122 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.119, D:D.122 NAG-NAG-FUC.10: 3 residues within 4Å: Chain E: N.119, D.156, N.158 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.8: 10 residues within 4Å: Chain A: X.101 Chain B: X.54 Chain E: E.76, T.77, N.79, M.80 Chain G: R.23, W.24, N.60, I.64 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:I.64 Hydrogen bonds: G:R.23, G:W.24

1 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.15: 12 residues within 4Å: Chain B: X.28 Chain E: M.75, Q.232, F.233, R.235, P.236, S.237 Chain G: N.106, S.108, V.129, G.132, Y.134 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain E Hydrophobic interactions: G:Y.134 Hydrogen bonds: E:F.233, E:R.235

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

NAG.17: 5 residues within 4Å: Chain C: K.88, N.89, N.90, S.91, H.92 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: M.80, N.99 Ligands: NAG-NAG.2 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain C: G.160, K.161, N.224, T.225, T.226 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain D: N.109, S.216, Y.217, Q.218 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain D: L.128, G.159, G.160, K.161, N.224, T.225 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain D: K.88, N.89, S.91, H.92 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain E: N.99, E.100 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain E: N.109, S.216, Y.217, Q.218 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain F: N.136 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain F: N.131 Ligand excluded by PLIP NAG.28: 7 residues within 4Å: Chain E: E.67, Q.69 Chain G: C.33, Y.112, N.114, H.115, T.121 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain G: N.136, T.138, H.139 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain E: C.207 Chain G: N.131 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain C: Q.69 Chain H: C.33, Y.112, N.114, H.115, T.116 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain H: N.136, T.138 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain H: C.101, N.131 Ligand excluded by 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

Rabbit polyclonal Fv heavy chain: A
Rabbit polyclonal Fv light chain: B
Glycoprotein GP1: CDE
Glycoprotein G2: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

D
A

E
B

F
a

G
b

H
c

Rabbit polyclonal Fv heavy chain

Rabbit polyclonal Fv light chain

Glycoprotein GP1

Glycoprotein G2

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