SMTL ID : 9miv.1

Native tagless Lassa virus spike complex pH 6.0

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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 NAG-NAG-BMA-MAN-NAG-MAN-MAN.20: 14 residues within 4Å: Chain C: M.75, G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain K: N.106, S.108, V.129, G.132, Y.134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.232 NAG-NAG-BMA-MAN-NAG-MAN-MAN.21: 13 residues within 4Å: Chain D: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain L: N.106, S.108, V.129, G.132, Y.134 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D: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: 6 residues within 4Å: Chain A: W.24, I.64 Chain B: E.76, T.77, N.79, M.80 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 F: D.93 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.116 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 G: D.93 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.116 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 H: D.93 1 PLIP interactions: 1 interactions with chain D Water bridges: D:K.116

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: 21 residues within 4Å: Chain B: K.88, N.89, S.91, H.92 Chain E: Q.1, V.2, E.27, S.28, F.32, Y.99, Y.101, F.103, A.104, Y.108, Y.110, D.112, V.113 Chain F: L.46, Y.49, A.55, T.56 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:Y.110, E:S.28, E:S.28, E:Q.1, E:Q.1, E:V.2, E:D.112, E:D.112, E:D.112, E:Q.1, E:V.2 Water bridges: E:R.97, E:E.27, E:E.27, E:R.97, E:Q.1, E:D.112, E:W.114, F:L.46 Hydrophobic interactions: F:A.55 NAG-NAG-BMA-MAN-NAG-GAL-MAN.10: 22 residues within 4Å: Chain C: K.88, N.89, S.91, H.92 Chain G: L.46, Y.49, A.55, T.56 Chain I: Q.1, V.2, E.27, S.28, F.32, R.97, Y.99, Y.101, F.103, A.104, Y.108, Y.110, D.112, V.113 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain G Hydrogen bonds: I:Y.110, I:S.28, I:S.28, I:D.112, I:D.112, I:D.112, I:Q.1, I:Q.1, I:V.2, I:V.2 Water bridges: I:R.97, I:R.97, I:R.97, I:D.112, G:L.46 Hydrophobic interactions: G: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 H: L.46, Y.49, A.55, T.56 Chain J: Q.1, V.2, E.27, S.28, F.32, Y.99, Y.101, F.103, A.104, Y.108, Y.110, D.112, V.113 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain H Hydrogen bonds: J:Y.110, J:S.28, J:S.28, J:D.112, J:D.112, J:D.112, J:Q.1, J:V.2, J:Q.3 Water bridges: J:R.97, J:R.97, J:D.112, J:W.114, H:L.46 Hydrophobic interactions: H:A.55, H: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: 11 residues within 4Å: Chain B: N.109, S.216, Y.217, Q.218 Chain E: A.104, W.105, N.107 Chain F: V.29, S.30, Y.32, G.66 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B Water bridges: F:Y.32, F:S.28, F:S.28, F:V.29, B:S.216, F:S.30, F:S.30, F:S.30 Hydrogen bonds: F: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: 7 residues within 4Å: Chain C: E.76, T.77, N.79, M.80, W.227 Chain K: W.24, I.64 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:W.24 Hydrophobic interactions: K:I.64 NAG-NAG-BMA-MAN.12: 6 residues within 4Å: Chain D: E.76, T.77, N.79, M.80 Chain L: W.24, I.64 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:W.24 Hydrophobic interactions: L: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: 9 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 Chain G: V.29, S.30 Chain I: A.104, W.105, N.107 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain C Water bridges: G:S.28, G:V.29, C:S.216, G:S.30, G:S.30 Hydrogen bonds: G:S.30 NAG-NAG-BMA-MAN-FUC.16: 10 residues within 4Å: Chain D: N.109, S.216, Y.217, Q.218 Chain H: S.28, V.29, S.30 Chain J: A.104, W.105, N.107 2 PLIP interactions: 2 interactions with chain H Water bridges: H:S.28, H:V.29, H:S.30 Hydrogen bonds: H:S.30

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

XYS-BDP-XYS.17: 5 residues within 4Å: Chain B: R.256, R.257, L.258 Chain C: Y.150 Chain D: S.121 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.257, B:R.257, B:L.258 Water bridges: B:L.258, C:S.255, C:R.256, C:R.256, C:R.256 Salt bridges: B:R.257 XYS-BDP-XYS.18: 6 residues within 4Å: Chain B: S.121 Chain C: R.256, R.257, L.258 Chain D: Y.150, R.256 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.257, C:R.257, C:L.258, D:R.256 Salt bridges: C:R.257 XYS-BDP-XYS.19: 6 residues within 4Å: Chain B: Y.150, R.256 Chain C: S.121 Chain D: R.256, R.257, L.258 7 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:R.257, D:R.257, D:L.258, B:R.256 Salt bridges: D:R.257 Water bridges: B:R.256, C:S.121

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.116 Chain B: Q.69 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.34, A:Y.112 Hydrogen bonds: A:K.32, A:N.114 Water bridges: A:C.33, A:G.119 NAG.23: 3 residues within 4Å: Chain A: S.130, N.131 Chain B: R.207 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.207, A:S.130, A:S.130 NAG.27: 6 residues within 4Å: Chain B: G.159, G.160, K.161, N.224, T.225, T.226 5 PLIP interactions: 5 interactions with chain B Water bridges: B:N.224, B:N.224, B:N.224, B:N.224, B:T.226 NAG.28: 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.29: 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:G.159, C:N.224, C:T.226 Water bridges: C:N.224, C:N.224 NAG.30: 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.31: 2 residues within 4Å: Chain D: N.99, E.100 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:E.100 Hydrogen bonds: D:E.100, D:E.100 Water bridges: D:N.99 NAG.32: 6 residues within 4Å: Chain D: G.159, G.160, K.161, N.224, T.225, T.226 5 PLIP interactions: 5 interactions with chain D Water bridges: D:N.224, D:N.224, D:N.224, D:N.224, D:T.226 NAG.33: 8 residues within 4Å: Chain C: Q.69 Chain K: K.32, C.33, F.34, Y.112, N.114, T.116, T.121 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:F.34, K:Y.112, K:T.121 Hydrogen bonds: K:K.32, K:N.114 Water bridges: K:C.33, K:G.119 NAG.34: 3 residues within 4Å: Chain K: S.130, N.131, L.135 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:L.135 Hydrogen bonds: K:S.130, K:S.130, K:N.131 NAG.35: 8 residues within 4Å: Chain D: Q.69 Chain L: K.32, C.33, F.34, Y.112, N.114, T.116, T.121 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:F.34, L:Y.112, L:T.121 Hydrogen bonds: L:K.32, L:N.114 Water bridges: L:C.33, L:G.119 NAG.36: 2 residues within 4Å: Chain L: S.130, N.131 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:S.130, L:S.130

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

UNX.24: 3 residues within 4Å: Chain A: H.46 Chain K: H.46 Chain L: H.46 No protein-ligand interaction detected (PLIP) UNX.25: 3 residues within 4Å: Chain A: G.1 Chain K: G.1 Chain L: G.1 No protein-ligand interaction detected (PLIP) UNX.26: 5 residues within 4Å: Chain A: M.161, Q.164 Chain K: M.161 Chain L: M.161, Q.164 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: AKL
Glycoprotein G1: BCD
12.1F Heavy chain: EIJ
12.1F Light chain: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

K
b

L
c

B
A

C
B

D
C

E
H

I
D

J
F

F
L

G
E

H
G

Glycoprotein G2

Glycoprotein G1

12.1F Heavy chain

12.1F Light chain

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