SMTL ID : 9mhe.1

Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

2 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.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.20: 14 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, S.133, Y.134 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.232

2 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 B: G.159, G.160, K.161, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain C: G.159, G.160, K.161, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP)

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.3: 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 Hydrogen bonds: A:W.24 Hydrophobic interactions: A:I.64 NAG-NAG-BMA.5: 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.11: 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.16: 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- FUC: 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-FUC.4: 5 residues within 4Å: Chain B: H.115, F.117, N.119, C.155, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.10: 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-FUC.15: 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.6: 23 residues within 4Å: Chain B: K.88, N.89, S.91, H.92 Chain G: Q.1, V.2, Q.3, E.27, S.28, F.32, Y.99, Y.101, F.103, A.104, Y.108, Y.110, D.112, V.113 Chain H: R.45, L.46, Y.49, A.55, T.56 10 PLIP interactions: 7 interactions with chain G, 3 interactions with chain H Water bridges: G:R.97, G:R.97, G:R.97, G:Y.110, G:D.112, G:W.114, H:R.45, H:T.56 Hydrogen bonds: G:E.27, G:E.27, G:S.28, G:Q.1, G:Q.1, G:D.112, G:D.112, G:D.112, G:Q.1, G:Q.1, G:V.2, G:V.2, G:Q.3, H:R.45 NAG-NAG-BMA-MAN-NAG-GAL-MAN.12: 23 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, Q.3, 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 K, 1 interactions with chain I Water bridges: K:E.27, K:R.97, K:Q.1, K:Q.1, K:R.97, K:R.97, I:T.56, I:T.56, K:D.112, K:W.114, I:L.46 Hydrogen bonds: K:E.27, K:S.28, K:D.112, K:D.112, K:D.112, K:Q.1, K:Q.1, K:V.2 NAG-NAG-BMA-MAN-NAG-GAL-MAN.17: 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, 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 L, 1 interactions with chain J Hydrogen bonds: L:Y.110, L:E.27, L:S.28, L:Q.1, L:Q.1, L:D.112, L:D.112, L:D.112, L:Q.1, L:V.2, L:V.2 Water bridges: L:R.97, L:R.97, L:D.112, L:W.114 Hydrophobic interactions: J:T.56

3 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.7: 9 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, S.30 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H, 1 interactions with chain B Water bridges: G:W.105, H:V.29, B:S.216 Hydrogen bonds: B:Q.218, H:S.30 NAG-NAG-BMA-MAN-FUC.13: 9 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 Chain I: S.28, S.30 Chain K: A.104, W.105, N.107 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain I, 1 interactions with chain C Water bridges: K:W.105, I:V.29 Hydrogen bonds: C:Q.218, I:S.30 NAG-NAG-BMA-MAN-FUC.18: 8 residues within 4Å: Chain D: N.109, S.216, Y.217, Q.218 Chain J: S.30 Chain L: A.104, W.105, N.107 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain J Water bridges: L:W.105, J:V.29 Hydrogen bonds: J: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.9: 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.14: 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 Hydrogen bonds: F:W.24, F:R.23 Hydrophobic interactions: F:I.64

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.19: 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 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.232 Water bridges: C:S.234

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

NAG.21: 6 residues within 4Å: Chain A: K.32, C.33, F.34, Y.112, N.114 Chain B: Q.69 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.34, A:Y.112 Hydrogen bonds: A:N.114, B:Q.69 Water bridges: A:L.31, A:K.32 NAG.22: 3 residues within 4Å: Chain A: S.130, N.131, L.135 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.135 Hydrogen bonds: A:S.130, A:S.130, A:N.131 NAG.25: 1 residues within 4Å: Chain B: N.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.99 Water bridges: B:N.99 NAG.26: 1 residues within 4Å: Chain C: N.99 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.99 NAG.27: 6 residues within 4Å: Chain D: G.159, G.160, K.161, N.224, T.225, T.226 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.224 Water bridges: D:L.128, D:G.160 NAG.28: 1 residues within 4Å: Chain D: N.99 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.99 NAG.29: 7 residues within 4Å: Chain C: Q.69 Chain E: K.32, C.33, F.34, Y.112, N.114, T.121 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:F.34, E:Y.112, E:T.121 Hydrogen bonds: E:K.32, E:N.114, C:Q.69 NAG.30: 3 residues within 4Å: Chain E: S.130, N.131, L.135 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.135 NAG.32: 6 residues within 4Å: Chain D: Q.69 Chain F: K.32, C.33, F.34, Y.112, N.114 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.34, F:Y.112 Hydrogen bonds: F:N.114 NAG.33: 3 residues within 4Å: Chain F: S.130, N.131, L.135 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.135 Hydrogen bonds: F:S.130, F:S.130, F:N.131

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

UNX.23: 3 residues within 4Å: Chain A: H.46 Chain E: H.46 Chain F: H.46 No protein-ligand interaction detected (PLIP) UNX.24: 3 residues within 4Å: Chain A: G.1 Chain E: G.1 Chain F: G.1 No protein-ligand interaction detected (PLIP)

1 x 01: (4S)-3-(4-tert-butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine

01.31: 18 residues within 4Å: Chain A: Y.160, R.163, Q.164, L.169, V.172, V.176 Chain C: L.23 Chain D: L.23 Chain E: Y.160, Q.164, L.169, V.172, D.173, V.176 Chain F: Y.160, R.163, Q.164, V.172 18 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C, 5 interactions with chain E, 3 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: A:Y.160, A:R.163, A:L.169, A:V.172, A:V.176, A:V.176, C:L.23, C:L.23, E:Y.160, E:L.169, E:V.176, F:Y.160, F:Y.160, D:L.23 Hydrogen bonds: A:R.163, E:Q.164, E:D.173, F:R.163

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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