SMTL ID : 8ejh.1

Lassa virus glycoprotein complex (Josiah) bound to 12.1F Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

12 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: 8 residues within 4Å: Chain A: E.76, T.77, N.79, M.80, N.99, W.227 Chain C: W.24, I.64 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.64 NAG-NAG-BMA.4: 7 residues within 4Å: Chain A: N.109, S.216, Y.217 Chain I: A.104, W.105, N.107 Chain J: S.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 9 residues within 4Å: Chain A: S.111, I.113, N.114, N.167, S.169, H.170, S.171, Y.219 Chain J: D.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain A: G.159, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 8 residues within 4Å: Chain B: E.76, T.77, N.79, M.80, N.99, W.227 Chain E: W.24, I.64 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.64 NAG-NAG-BMA.11: 7 residues within 4Å: Chain B: N.109, S.216, Y.217 Chain K: A.104, W.105, N.107 Chain L: S.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 9 residues within 4Å: Chain B: S.111, I.113, N.114, N.167, S.169, H.170, S.171, Y.219 Chain L: D.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain B: G.159, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 8 residues within 4Å: Chain D: E.76, T.77, N.79, M.80, N.99, W.227 Chain F: W.24, I.64 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.64 NAG-NAG-BMA.20: 7 residues within 4Å: Chain D: N.109, S.216, Y.217 Chain G: A.104, W.105, N.107 Chain H: S.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 9 residues within 4Å: Chain D: S.111, I.113, N.114, N.167, S.169, H.170, S.171, Y.219 Chain H: D.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 4 residues within 4Å: Chain D: G.159, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP)

3 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.2: 13 residues within 4Å: Chain A: K.88, N.89, N.90, S.91, H.92 Chain I: L.4, F.32, Y.99, Y.101, D.112, V.113 Chain J: T.56 Ligands: MAN.35 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:Y.99, I:L.4, J:T.56, J:T.56 NAG-NAG-BMA-MAN-MAN.9: 13 residues within 4Å: Chain B: K.88, N.89, N.90, S.91, H.92 Chain K: L.4, F.32, Y.99, Y.101, D.112, V.113 Chain L: T.56 Ligands: MAN.36 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain L Hydrogen bonds: K:Y.99, K:L.4, L:T.56, L:T.56 NAG-NAG-BMA-MAN-MAN.18: 13 residues within 4Å: Chain D: K.88, N.89, N.90, S.91, H.92 Chain G: L.4, F.32, Y.99, Y.101, D.112, V.113 Chain H: T.56 Ligands: MAN.34 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:Y.99, H:T.56, H:T.56, G:L.4

9 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 2 residues within 4Å: Chain A: M.80, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: H.115, F.117, N.119, C.155, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: M.80, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain B: H.115, F.117, N.119, C.155, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain C: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain D: M.80, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain D: H.115, F.117, N.119, C.155, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain E: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 6 residues within 4Å: Chain F: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(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-MAN-MAN-MAN.15: 13 residues within 4Å: Chain A: M.75, Y.200, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain C: N.106, S.108, G.132, Y.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.232 NAG-NAG-BMA-MAN-MAN-MAN-MAN.24: 13 residues within 4Å: Chain B: M.75, Y.200, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain E: N.106, S.108, G.132, Y.134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.232 NAG-NAG-BMA-MAN-MAN-MAN-MAN.26: 13 residues within 4Å: Chain D: M.75, Y.200, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain F: N.106, S.108, G.132, Y.134 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.232

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

NAG.28: 3 residues within 4Å: Chain C: C.101, S.130, N.131 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.130, C:N.131 NAG.29: 2 residues within 4Å: Chain C: N.136, H.139 No protein-ligand interaction detected (PLIP) NAG.30: 3 residues within 4Å: Chain E: C.101, S.130, N.131 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.130, E:N.131 NAG.31: 2 residues within 4Å: Chain E: N.136, H.139 No protein-ligand interaction detected (PLIP) NAG.32: 3 residues within 4Å: Chain F: C.101, S.130, N.131 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.130, F:N.131 NAG.33: 2 residues within 4Å: Chain F: N.136, H.139 No protein-ligand interaction detected (PLIP)

3 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.34: 3 residues within 4Å: Chain G: E.27, S.28 Ligands: NAG-NAG-BMA-MAN-MAN.18 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:E.27, G:S.28 MAN.35: 3 residues within 4Å: Chain I: E.27, S.28 Ligands: NAG-NAG-BMA-MAN-MAN.2 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:E.27, I:S.28 MAN.36: 3 residues within 4Å: Chain K: E.27, S.28 Ligands: NAG-NAG-BMA-MAN-MAN.9 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:E.27, K:S.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perrett, H.R. et al., Structural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies. Cell Rep (2023)

Release Date

2023-06-07

Peptides

Glycoprotein G1: ABD
Glycoprotein G2: CEF
12.1F Fab heavy chain: GIK
12.1F Fab light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

D
A

C
c

E
b

F
a

G
H

I
J

K
h

H
L

J
K

L
l

Glycoprotein G1

Glycoprotein G2

12.1F Fab heavy chain

12.1F Fab light chain

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