SMTL ID : 7s8h.1

Structure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-3-3-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN: 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.1: 10 residues within 4Å: Chain A: E.18, T.19, N.21, M.22 Chain D: M.101 Chain F: R.23, W.24, I.64 Chain I: D.62 Ligands: NAG-NAG-FUC.3 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain F Hydrogen bonds: I:D.62 Hydrophobic interactions: F:I.64 NAG-NAG-BMA-MAN.11: 10 residues within 4Å: Chain G: E.18, T.19, N.21, M.22 Chain J: M.101 Chain L: R.23, W.24, I.64 Chain O: D.62 Ligands: NAG-NAG-FUC.13 2 PLIP interactions: 1 interactions with chain O, 1 interactions with chain L Hydrogen bonds: O:D.62 Hydrophobic interactions: L:I.64 NAG-NAG-BMA-MAN.21: 10 residues within 4Å: Chain C: D.62 Chain M: E.18, T.19, N.21, M.22 Chain P: M.101 Chain R: R.23, W.24, I.64 Ligands: NAG-NAG-FUC.23 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain R Hydrogen bonds: C:D.62 Hydrophobic interactions: R:I.64

15 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: 6 residues within 4Å: Chain A: K.30, N.31, S.33, H.34 Chain D: S.54, G.55 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.51, S.158, Y.159, Q.160 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: S.53, I.55, Q.107, N.109, S.111, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: G.101, G.102, K.103, N.166, T.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain A: Q.11 Chain F: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain G: K.30, N.31, S.33, H.34 Chain J: S.54, G.55 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain G: N.51, S.158, Y.159, Q.160 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain G: S.53, I.55, Q.107, N.109, S.111, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain G: G.101, G.102, K.103, N.166, T.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 7 residues within 4Å: Chain G: Q.11 Chain L: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 6 residues within 4Å: Chain M: K.30, N.31, S.33, H.34 Chain P: S.54, G.55 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain M: N.51, S.158, Y.159, Q.160 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 6 residues within 4Å: Chain M: S.53, I.55, Q.107, N.109, S.111, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 6 residues within 4Å: Chain M: G.101, G.102, K.103, N.166, T.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 7 residues within 4Å: Chain M: Q.11 Chain R: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP)

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: 4 residues within 4Å: Chain A: M.22, N.41, E.42 Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.13: 4 residues within 4Å: Chain G: M.22, N.41, E.42 Ligands: NAG-NAG-BMA-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.23: 4 residues within 4Å: Chain M: M.22, N.41, E.42 Ligands: NAG-NAG-BMA-MAN.21 No protein-ligand interaction detected (PLIP)

6 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.5: 3 residues within 4Å: Chain A: H.57, F.59, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUC.9: 8 residues within 4Å: Chain C: D.2, Q.28, I.31, Y.92, G.94, S.95 Chain F: N.136, H.139 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.2, C:D.2, C:Q.28 NAG-NAG-BMA-MAN-MAN-FUC.15: 3 residues within 4Å: Chain G: H.57, F.59, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUC.19: 8 residues within 4Å: Chain I: D.2, Q.28, I.31, Y.92, G.94, S.95 Chain L: N.136, H.139 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.2, I:D.2, I:Q.28 NAG-NAG-BMA-MAN-MAN-FUC.25: 3 residues within 4Å: Chain M: H.57, F.59, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUC.29: 8 residues within 4Å: Chain O: D.2, Q.28, I.31, Y.92, G.94, S.95 Chain R: N.136, H.139 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:D.2, O:D.2, O:Q.28

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

NAG.10: 3 residues within 4Å: Chain C: S.29, G.70 Chain F: N.131 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.29, C:S.29 NAG.20: 3 residues within 4Å: Chain I: S.29, G.70 Chain L: N.131 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.29, I:S.29 NAG.30: 3 residues within 4Å: Chain O: S.29, G.70 Chain R: N.131 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:S.29, O:S.29

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: AGM
18.5C Fab Heavy Chain: BHN
18.5C Fab Light Chain: CIO
36.1F Fab Heavy Chain: DJP
36.1F Fab Light Chain: EKQ
Glycoprotein G2: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
A

M
A

B
H

H
H

N
H

C
L

I
L

O
L

D
B

J
B

P
B

E
C

K
C

Q
C

F
a

L
a

R
a

Glycoprotein G1

18.5C Fab Heavy Chain

18.5C Fab Light Chain

36.1F Fab Heavy Chain

36.1F Fab Light Chain

Glycoprotein G2

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