SMTL ID : 9mj2.1

Flag-tag Lassa virus spike complex at pH 6.0

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

6 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.1: 5 residues within 4Å: Chain A: E.18, T.19, N.21 Chain B: W.24, I.64 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.64 NAG-NAG-BMA.3: 6 residues within 4Å: Chain A: S.53, I.55, K.58, N.109, S.111, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 6 residues within 4Å: Chain C: W.24, I.64 Chain E: E.18, T.19, N.21, M.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.24 Hydrophobic interactions: C:I.64 NAG-NAG-BMA.13: 6 residues within 4Å: Chain E: S.53, I.55, K.58, N.109, S.111, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 6 residues within 4Å: Chain D: W.24, I.64 Chain F: E.18, T.19, N.21, M.22 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.64 NAG-NAG-BMA.17: 7 residues within 4Å: Chain F: S.53, I.55, K.58, Q.107, N.109, S.111, Y.161 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.2: 4 residues within 4Å: Chain A: H.57, F.59, N.61, N.100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.12: 5 residues within 4Å: Chain E: H.57, F.59, N.61, D.98, N.100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.16: 5 residues within 4Å: Chain F: H.57, F.59, N.61, D.98, N.100 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.4: 4 residues within 4Å: Chain A: N.51, S.158, Y.159, Q.160 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.14: 4 residues within 4Å: Chain E: N.51, S.158, Y.159, Q.160 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.18: 4 residues within 4Å: Chain F: N.51, S.158, Y.159, Q.160 No protein-ligand interaction detected (PLIP)

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

XYS-BDP-XYS.5: 5 residues within 4Å: Chain A: R.198, R.199, L.200 Chain E: Y.92 Chain F: S.63 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.199, A:R.199, A:L.200 Salt bridges: A:R.198, A:R.199 XYS-BDP-XYS.6: 5 residues within 4Å: Chain A: S.63 Chain E: R.198, R.199, L.200 Chain F: Y.92 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.198, E:R.199, E:R.199, E:L.200, E:R.198 Salt bridges: E:R.198, E:R.199 XYS-BDP-XYS.7: 5 residues within 4Å: Chain A: Y.92 Chain E: S.63 Chain F: R.198, R.199, L.200 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.199, F:R.199, F:L.200 Salt bridges: F:R.199

3 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.8: 12 residues within 4Å: Chain A: D.171, C.173, Q.174, F.175, S.176, R.177, S.179 Chain B: N.106, S.108, V.129, G.132, Y.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.174, A:C.173, A:Q.174 NAG-NAG-BMA-MAN.9: 12 residues within 4Å: Chain C: N.106, S.108, V.129, G.132, Y.134 Chain E: D.171, C.173, Q.174, F.175, S.176, R.177, S.179 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.174, E:Q.174 NAG-NAG-BMA-MAN.10: 12 residues within 4Å: Chain D: N.106, S.108, V.129, G.132, Y.134 Chain F: D.171, C.173, Q.174, F.175, S.176, R.177, S.179 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.174, F:D.171, F:Q.174

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

NAG.19: 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.20: 6 residues within 4Å: Chain A: K.30, N.31, N.32, S.33, H.34, Y.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.33, A:S.33 NAG.21: 3 residues within 4Å: Chain A: M.22, N.41, E.42 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.41, A:E.42, A:E.42 NAG.22: 7 residues within 4Å: Chain A: Q.11 Chain B: K.32, F.34, Y.112, N.114, T.116, T.121 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.34, B:Y.112, B:T.121 Hydrogen bonds: B:N.114 NAG.23: 2 residues within 4Å: Chain B: S.130, N.131 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.149, B:S.130, B:S.130 NAG.27: 7 residues within 4Å: Chain C: K.32, C.33, Y.112, N.114, T.116, T.121 Chain E: Q.11 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.32, C:Y.112 Hydrogen bonds: C:K.32 NAG.28: 3 residues within 4Å: Chain C: S.130, N.131 Chain E: R.149 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:S.130, C:S.130, E:R.149, E:R.149 NAG.29: 5 residues within 4Å: Chain D: K.32, Y.112, N.114, T.121 Chain F: Q.11 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.112, D:T.121 NAG.30: 1 residues within 4Å: Chain D: N.131 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:R.149, D:S.130, D:S.130, D:N.131 NAG.31: 6 residues within 4Å: Chain E: G.101, G.102, K.103, N.166, T.167, T.168 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.166 NAG.32: 5 residues within 4Å: Chain E: K.30, N.31, S.33, H.34, Y.159 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.33 NAG.33: 2 residues within 4Å: Chain E: M.22, N.41 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.41 NAG.34: 5 residues within 4Å: Chain F: G.101, K.103, N.166, T.167, T.168 No protein-ligand interaction detected (PLIP) NAG.35: 5 residues within 4Å: Chain F: K.30, N.31, N.32, S.33, H.34 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.33 NAG.36: 3 residues within 4Å: Chain F: M.22, N.41, E.42 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:E.42 Hydrogen bonds: F:E.42, F:E.42

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

UNX.24: 4 residues within 4Å: Chain B: M.161 Chain C: M.161, Q.164 Chain D: M.161 No protein-ligand interaction detected (PLIP) UNX.25: 3 residues within 4Å: Chain B: H.46 Chain C: H.46 Chain D: H.46 No protein-ligand interaction detected (PLIP) UNX.26: 3 residues within 4Å: Chain B: G.1 Chain C: G.1 Chain D: 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

Pre-glycoprotein polyprotein GP complex: AEF
Glycoprotein G2: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
B

F
C

B
a

C
b

D
c

Pre-glycoprotein polyprotein GP complex

Glycoprotein G2

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