SMTL ID : 9mj1.1

Native tagless Lassa virus spike complex bound at pH 8.0

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- MAN- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-NAG-MAN-MAN.1: 13 residues within 4Å: Chain A: N.106, S.108, V.129, G.132, Y.134 Chain B: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.232

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.2: 7 residues within 4Å: Chain A: W.24, I.64 Chain B: E.76, T.77, N.79, M.80, W.227 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.64 NAG-NAG-BMA.4: 9 residues within 4Å: Chain B: S.111, I.113, N.114, K.116, Q.165, N.167, S.169, Y.219 Chain H: D.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 9 residues within 4Å: Chain C: S.111, I.113, N.114, K.116, Q.165, N.167, S.169, Y.219 Chain I: D.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 9 residues within 4Å: Chain D: S.111, I.113, N.114, K.116, Q.165, N.167, S.169, Y.219 Chain J: D.93 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- FUC: 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-FUC.3: 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-BMA-MAN-FUC.8: 6 residues within 4Å: Chain C: H.115, F.117, N.119, C.155, D.156, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.13: 6 residues within 4Å: Chain D: H.115, F.117, N.119, C.155, D.156, N.158 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- NAG- GAL- MAN: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(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-NAG-GAL-MAN.5: 20 residues within 4Å: Chain B: K.88, N.89, S.91, H.92 Chain G: Q.1, V.2, E.27, S.28, F.32, Y.99, Y.101, F.103, A.104, Y.110, D.112, V.113 Chain H: L.46, Y.49, A.55, T.56 8 PLIP interactions: 6 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:Y.110, G:S.28, G:Q.1, G:Q.1, G:V.2, G:D.112, G:D.112, G:D.112, G:Q.1, G:Q.1, G:V.2, G:V.2 Water bridges: G:R.97, G:E.27, G:E.27, G:S.28, G:S.28, G:S.28, H:T.56, H:L.46, H:T.56, G:D.112, G:W.114 Hydrophobic interactions: H:A.55 NAG-NAG-BMA-MAN-NAG-GAL-MAN.10: 21 residues within 4Å: Chain C: K.88, N.89, S.91, H.92 Chain I: L.46, Y.49, A.55, T.56 Chain K: Q.1, V.2, E.27, S.28, F.32, R.97, Y.99, Y.101, F.103, A.104, Y.110, D.112, V.113 7 PLIP interactions: 6 interactions with chain K, 1 interactions with chain I Water bridges: K:R.97, K:E.27, K:E.27, K:E.27, I:T.56, I:T.56, K:D.112, K:W.114 Hydrogen bonds: K:S.28, K:S.28, K:D.112, K:D.112, K:D.112, K:Q.1, K:Q.1, K:V.2, K:V.2 Hydrophobic interactions: I:A.55 NAG-NAG-BMA-MAN-NAG-GAL-MAN.15: 21 residues within 4Å: Chain D: K.88, N.89, S.91, H.92 Chain J: L.46, Y.49, A.55, T.56 Chain L: Q.1, V.2, Q.3, E.27, S.28, F.32, Y.99, Y.101, F.103, A.104, Y.110, D.112, V.113 9 PLIP interactions: 7 interactions with chain L, 2 interactions with chain J Hydrogen bonds: L:Y.110, L:S.28, L:S.28, L:D.112, L:D.112, L:D.112, L:Q.1, L:V.2, L:V.2, L:Q.3 Water bridges: L:R.97, J:T.56, J:T.56, J:L.46, J:T.56, L:Q.1, L:D.112, L:W.114 Hydrophobic interactions: J:A.55, J:T.56

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-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.6: 12 residues within 4Å: Chain B: N.109, S.216, Y.217, Q.218 Chain G: A.104, W.105, N.107 Chain H: S.28, V.29, S.30, Y.32, G.66 8 PLIP interactions: 7 interactions with chain H, 1 interactions with chain B Water bridges: H:S.67, H:G.66, H:G.66, H:G.66, H:S.67, H:S.28, H:V.29, H:Y.32, B:S.216, H:S.30, H:S.30, H:S.30, H:S.30, H:S.30, H:S.30, B:Q.218 Hydrogen bonds: H:S.30

2 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.7: 6 residues within 4Å: Chain C: E.76, T.77, N.79, M.80 Chain E: W.24, I.64 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:W.24 Hydrophobic interactions: E:I.64 NAG-NAG-BMA-MAN.12: 7 residues within 4Å: Chain D: E.76, T.77, N.79, M.80 Chain F: R.23, W.24, I.64 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.64

2 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-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-FUC.11: 10 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 Chain I: S.28, V.29, S.30 Chain K: A.104, W.105, N.107 7 PLIP interactions: 7 interactions with chain I Water bridges: I:S.67, I:S.28, I:V.29, I:S.30, I:S.30, I:S.30, I:S.30, I:S.30, I:S.30 Hydrogen bonds: I:S.30 NAG-NAG-BMA-MAN-FUC.16: 10 residues within 4Å: Chain D: N.109, S.216, Y.217, Q.218 Chain J: S.28, V.29, S.30 Chain L: A.104, W.105, N.107 7 PLIP interactions: 6 interactions with chain J, 1 interactions with chain D Water bridges: J:S.28, J:S.28, J:V.29, D:Q.218, J:S.30, J:S.30, J:S.30, J:S.30, J:S.30 Hydrogen bonds: J:S.30

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.17: 13 residues within 4Å: Chain C: 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 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:Q.232 Water bridges: C:F.233, C:S.234, C:R.235, C:R.235, E:G.132

1 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(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-NAG-MAN.18: 13 residues within 4Å: Chain D: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain F: N.106, S.108, V.129, G.132, Y.134 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.232

3 x XYS- BDP- XYS: alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose

XYS-BDP-XYS.19: 5 residues within 4Å: Chain B: R.256, R.257, L.258 Chain C: Y.150 Chain D: S.121 6 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:R.257, B:R.257, B:L.258, D:S.121 Salt bridges: B:R.257 Water bridges: C:R.256 XYS-BDP-XYS.20: 7 residues within 4Å: Chain B: S.121 Chain C: R.256, R.257, L.258 Chain D: Y.150, R.256 Ligands: XYS-BDP-XYS.21 8 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C, 1 interactions with chain B Water bridges: D:Y.150, D:R.256, D:R.256 Hydrogen bonds: C:R.257, C:R.257, C:L.258, B:S.121, D:R.256 Salt bridges: C:R.257 XYS-BDP-XYS.21: 7 residues within 4Å: Chain B: Y.150, R.256 Chain C: S.121 Chain D: R.256, R.257, L.258 Ligands: XYS-BDP-XYS.20 8 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: D:R.257, D:R.257, D:L.258, B:R.256, C:S.121, C:S.121 Salt bridges: D:R.257 Water bridges: B:R.256

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

NAG.22: 7 residues within 4Å: Chain A: K.32, C.33, F.34, Y.112, N.114, T.121 Chain B: Q.69 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.34, A:Y.112, A:T.121 Hydrogen bonds: A:N.114 Water bridges: A:K.32, B:Q.69, B:Q.69, B:Q.69 NAG.23: 3 residues within 4Å: Chain A: S.130, N.131, L.135 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.135 Hydrogen bonds: A:S.130, A:S.130, A:N.131 Water bridges: A:S.130 NAG.26: 6 residues within 4Å: Chain B: G.159, G.160, K.161, N.224, T.225, T.226 6 PLIP interactions: 6 interactions with chain B Water bridges: B:L.128, B:N.224, B:N.224, B:N.224, B:N.224, B:T.226 NAG.27: 2 residues within 4Å: Chain B: N.99, E.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.99, B:E.100, B:E.100 NAG.28: 6 residues within 4Å: Chain C: G.159, G.160, K.161, N.224, T.225, T.226 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.224 Water bridges: C:G.159, C:N.224, C:T.225, C:T.226 NAG.29: 2 residues within 4Å: Chain C: N.99, E.100 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.99, C:E.100 NAG.30: 2 residues within 4Å: Chain D: N.99, E.100 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:E.100 Hydrogen bonds: D:E.100, D:E.100 Water bridges: D:N.99, D:N.99 NAG.31: 6 residues within 4Å: Chain D: G.159, G.160, K.161, N.224, T.225, T.226 6 PLIP interactions: 6 interactions with chain D Water bridges: D:L.128, D:N.224, D:N.224, D:N.224, D:N.224, D:T.225 NAG.32: 6 residues within 4Å: Chain C: Q.69 Chain E: K.32, C.33, Y.112, N.114, T.121 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain E Water bridges: C:Q.69, C:Q.69, C:Q.69, E:L.31 Hydrophobic interactions: E:Y.112, E:T.121 Hydrogen bonds: E:N.114 NAG.33: 3 residues within 4Å: Chain E: S.130, N.131, L.135 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.135 Hydrogen bonds: E:S.130, E:S.130, E:N.131 NAG.34: 7 residues within 4Å: Chain D: Q.69 Chain F: K.32, C.33, F.34, Y.112, N.114, T.121 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:F.34, F:Y.112, F:T.121 Hydrogen bonds: F:N.114 Water bridges: F:K.32, F:K.32, F:C.33, F:C.33, D:E.67, D:Q.69 NAG.35: 3 residues within 4Å: Chain F: S.130, N.131, L.135 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.135 Hydrogen bonds: F:S.130, F:N.131

2 x UNX: UNKNOWN LIGAND(Non-functional Binders)

UNX.24: 3 residues within 4Å: Chain A: H.46 Chain E: H.46 Chain F: H.46 No protein-ligand interaction detected (PLIP) UNX.25: 3 residues within 4Å: Chain A: G.1 Chain E: G.1 Chain F: G.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katz, M. et al., pH-induced conformational changes and inhibition of the Lassa virus spike complex. Cell Host Microbe (2025)

Release Date

2025-08-27

Peptides

Glycoprotein G2: AEF
Glycoprotein G1: BCD
12.1F Heavy chain: GKL
12.1F Light chain: HIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

E
b

F
c

B
A

C
B

D
C

G
H

K
D

L
F

H
L

I
E

J
G

Membrane

We predict this structure to be a membrane protein.
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Glycoprotein G2

Glycoprotein G1

12.1F Heavy chain

12.1F Light chain

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