SMTL ID : 9r8u.1

Flag-tag LASV spike acidified to pH 5.0 and re-equilibrated to pH 8.0

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: 7 residues within 4Å: Chain A: E.76, T.77, N.79, M.80, N.99 Chain B: W.24, I.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.24 Hydrophobic interactions: B:I.64 NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: I.113, N.114, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 7 residues within 4Å: Chain C: W.24, I.64 Chain E: E.76, T.77, N.79, M.80, W.227 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.24 Hydrophobic interactions: C:I.64 NAG-NAG-BMA.10: 6 residues within 4Å: Chain E: S.111, I.113, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 7 residues within 4Å: Chain D: W.24, I.64 Chain F: E.76, T.77, N.79, M.80, W.227 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.24 Hydrophobic interactions: D:I.64 NAG-NAG-BMA.14: 5 residues within 4Å: Chain F: I.113, Q.165, N.167, S.169, Y.219 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: 5 residues within 4Å: Chain A: H.115, F.117, N.119, C.155, D.156 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.9: 5 residues within 4Å: Chain E: H.115, F.117, N.119, C.155, D.156 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.13: 4 residues within 4Å: Chain F: H.115, F.117, N.119, D.156 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.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.11: 4 residues within 4Å: Chain E: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 3 residues within 4Å: Chain F: N.109, S.216, Y.217 No protein-ligand interaction detected (PLIP)

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.5: 11 residues within 4Å: Chain A: D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain B: N.106, S.108, G.132, Y.134 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.232, A:R.235 Hydrophobic interactions: B:Y.134 NAG-NAG-BMA-MAN.6: 11 residues within 4Å: Chain C: N.106, S.108, G.132, Y.134 Chain E: D.229, C.231, Q.232, F.233, S.234, R.235, S.237 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.232, E:D.229, E:Q.232 NAG-NAG-BMA-MAN.7: 12 residues within 4Å: Chain D: N.106, S.108, V.129, G.132, Y.134 Chain F: D.229, C.231, Q.232, F.233, S.234, R.235, S.237 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:Q.232, F:D.229, F:D.229 Hydrophobic interactions: D:Y.134

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

NAG.16: 4 residues within 4Å: Chain A: G.159, N.224, T.225, T.226 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.226 NAG.17: 5 residues within 4Å: Chain A: K.88, N.89, N.90, S.91, H.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.91, A:S.91 NAG.18: 2 residues within 4Å: Chain A: N.99, E.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.100, A:E.100 NAG.19: 6 residues within 4Å: Chain A: Q.69 Chain B: K.32, C.33, Y.112, N.114, T.116 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.112 Hydrogen bonds: B:N.114, A:Q.69 NAG.20: 2 residues within 4Å: Chain B: S.130, N.131 No protein-ligand interaction detected (PLIP) NAG.23: 5 residues within 4Å: Chain C: K.32, Y.112, N.114, T.121 Chain E: Q.69 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.112, C:T.121 NAG.24: 2 residues within 4Å: Chain C: S.130, N.131 No protein-ligand interaction detected (PLIP) NAG.25: 5 residues within 4Å: Chain D: K.32, Y.112, N.114, T.121 Chain F: Q.69 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.112 NAG.26: 2 residues within 4Å: Chain D: S.130, N.131 No protein-ligand interaction detected (PLIP) NAG.27: 4 residues within 4Å: Chain E: G.159, G.160, K.161, N.224 No protein-ligand interaction detected (PLIP) NAG.28: 4 residues within 4Å: Chain E: N.89, S.91, H.92, Y.217 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.91 NAG.29: 2 residues within 4Å: Chain E: N.99, E.100 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.100, E:E.100 NAG.30: 5 residues within 4Å: Chain F: G.159, K.161, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG.31: 5 residues within 4Å: Chain F: K.88, N.89, N.90, S.91, H.92 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.88, F:K.88, F:N.89, F:S.91 NAG.32: 2 residues within 4Å: Chain F: N.99, E.100 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.99, F:E.100

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

UNX.21: 3 residues within 4Å: Chain B: H.46 Chain C: H.46 Chain D: H.46 No protein-ligand interaction detected (PLIP) UNX.22: 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

2025-09-17

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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