SMTL ID : 8t5c.1

Lassa GPC Trimer in complex with Fab 8.11G and nanobody D5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-2-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.1: 16 residues within 4Å: Chain A: E.18, T.19, N.21, M.22, G.40, N.41 Chain B: W.24, I.64 Chain J: Y.105 Chain K: Y.50, G.51, Y.53, T.54, R.55, S.64 Ligands: NAG-NAG-BMA-MAN-MAN.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain K Hydrophobic interactions: B:I.64 Hydrogen bonds: K:T.54

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: 4 residues within 4Å: Chain A: H.57, F.59, N.61, N.100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain C: F.59, N.61, D.64, N.100 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.59 NAG-NAG-BMA.13: 3 residues within 4Å: Chain E: F.59, N.61, N.100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 6 residues within 4Å: Chain E: Q.11 Chain F: K.32, Y.112, N.114, G.119, T.121 No protein-ligand interaction detected (PLIP)

3 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-BMA.3: 4 residues within 4Å: Chain A: D.117, S.159, Q.161 Ligands: NAG.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.117 Hydrogen bonds: A:D.117 NAG-BMA.4: 3 residues within 4Å: Chain A: H.112, S.113 Ligands: NAG.21 No protein-ligand interaction detected (PLIP) NAG-BMA.14: 3 residues within 4Å: Chain E: H.112, S.113 Ligands: NAG.35 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.112, E:S.113

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.5: 14 residues within 4Å: Chain A: M.17, D.172, Q.175, F.176, S.177, R.178, P.179, S.180 Chain B: N.106, S.108, V.129, S.133, Y.134 Chain K: D.58 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain K Hydrogen bonds: A:Q.175, A:D.172, K:D.58, A:R.178 NAG-NAG-BMA-MAN-MAN-MAN.10: 12 residues within 4Å: Chain C: M.17, Q.175, F.176, S.177, R.178, S.180 Chain D: N.106, S.108, V.129, S.133, Y.134 Chain I: D.58 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.175, C:K.30, D:Y.134 NAG-NAG-BMA-MAN-MAN-MAN.15: 15 residues within 4Å: Chain E: M.17, N.31, D.172, C.174, Q.175, F.176, S.177, R.178, P.179, S.180 Chain F: N.106, S.108, V.129, S.133, Y.134 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.175, E:D.172, E:C.174, E:Q.175, E:R.178, E:R.178

2 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.6: 10 residues within 4Å: Chain A: Q.11 Chain B: K.32, C.33, F.34, Y.112, N.114, T.116, T.121 Chain J: Y.102 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Y.102, J:Y.102 NAG-NAG-BMA-MAN-MAN.11: 8 residues within 4Å: Chain D: L.31, C.33, F.34, Y.112, N.114, T.116, T.121 Chain H: Y.102 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.7: 20 residues within 4Å: Chain C: E.18, T.19, N.21, M.22, N.41 Chain D: T.22, W.24, I.64 Chain H: Y.105 Chain I: D.32, K.33, Y.50, G.51, Y.53, T.54, R.55, P.61, Y.92 Ligands: MAN-MAN-MAN.8, MAN-MAN-MAN.8 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain I, 2 interactions with chain H Hydrogen bonds: D:W.24, I:D.32, H:Y.105, H:Y.105, I:T.54 Hydrophobic interactions: D:I.64

1 x MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose

MAN-MAN-MAN.8: 7 residues within 4Å: Chain I: Y.53, R.55, S.64 Ligands: NAG-NAG-BMA-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN.7, NAG.24 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.12: 8 residues within 4Å: Chain E: E.18, T.19, N.21, M.22, W.170 Chain F: R.23, W.24, I.64 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.64

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

NAG.17: 2 residues within 4Å: Chain A: N.41 Chain K: R.78 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: K.103, N.167, T.168, T.169 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: K.30, N.31, N.32, S.33, H.34 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.51, S.159, Q.161 Ligands: NAG-BMA.3 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain A: K.58, N.109, H.112, S.113, Y.162 Ligands: NAG-BMA.4 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: S.130, N.131 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.136 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: N.41, E.42 Ligands: MAN-MAN-MAN.8 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain C: K.58, Q.107, N.109, H.112, Y.162 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain C: G.101, G.102, K.103, N.167, T.168 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: N.31, N.32, S.33, H.34 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.51, S.159, Y.160, Q.161 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain D: S.130, N.131, G.132 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain D: N.136 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain E: G.40, N.41 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: K.103, N.167, T.168 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain E: K.30, N.31, N.32, S.33, H.34 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain E: N.51, S.159, Y.160, Q.161 Ligand excluded by PLIP NAG.35: 7 residues within 4Å: Chain E: H.57, K.58, N.109, H.112, S.113, Y.162 Ligands: NAG-BMA.14 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: S.147 Chain F: N.131, G.132 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain F: N.136 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain I: L.12, S.21, S.23, N.73 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain K: S.21, S.23, N.73 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, J. et al., Cleavage-intermediate Lassa virus trimer elicits neutralizing responses, identifies neutralizing nanobodies, and reveals an apex-situated site-of-vulnerability. Nat Commun (2024)

Release Date

2024-01-03

Peptides

Glycoprotein G1: ACE
Glycoprotein G2: BDF
D5 nanobody: G
8.11G Heavy Chain: HJ
8.11G Light Chain: IK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
A

E
C

B
b

D
a

F
c

G
D

H
H

J
E

I
L

K
I

Glycoprotein G1

Glycoprotein G2

D5 nanobody

8.11G Heavy Chain

8.11G Light Chain