SMTL ID : 7uot.1

Native Lassa glycoprotein in complex with neutralizing antibodies 8.9F and 37.2D

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-1-1-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, W.227 Chain B: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 7 residues within 4Å: Chain A: S.111, I.113, K.116, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 7 residues within 4Å: Chain E: S.111, I.113, K.116, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 6 residues within 4Å: Chain I: E.76, T.77, N.79, N.99, W.227 Chain J: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 5 residues within 4Å: Chain I: K.116, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 4 residues within 4Å: Chain I: G.159, G.160, K.161, N.224 No protein-ligand interaction detected (PLIP)

11 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: 4 residues within 4Å: Chain A: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: G.159, G.160, K.161, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain A: Q.69 Chain B: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain E: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain E: G.159, G.160, K.161, N.224, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain E: Q.69 Chain F: K.32, C.33, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain I: K.88, N.89, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain I: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain J: K.32, C.33, Y.112, N.114 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: 4 residues within 4Å: Chain A: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.13: 4 residues within 4Å: Chain E: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.23: 3 residues within 4Å: Chain I: N.109, S.216, Y.217 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[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-MAN-FUC.5: 9 residues within 4Å: Chain A: H.115, F.117, N.119 Chain M: S.55, S.57, I.72, D.73, T.74, Y.109 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:S.55, M:S.55, M:S.55, M:D.73, M:D.73 NAG-NAG-BMA-MAN-MAN-FUC.11: 8 residues within 4Å: Chain B: W.127, L.135, N.136, E.137 Chain H: N.55, G.56, Y.57, T.58 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:N.55, H:T.58 Hydrophobic interactions: H:Y.57 NAG-NAG-BMA-MAN-MAN-FUC.22: 6 residues within 4Å: Chain F: N.136, E.137 Chain L: N.55, G.56, Y.57, T.58 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:T.58 NAG-NAG-BMA-MAN-MAN-FUC.29: 13 residues within 4Å: Chain I: H.115, N.119, D.122, K.126 Chain M: Y.123 Chain N: A.33, F.34, Y.51, E.52, V.53, S.55, R.56, K.68 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain I Hydrogen bonds: N:E.52, N:E.52, N:S.55, I:K.126, N:F.34, N:Y.51, N:Y.51, N:R.56, N:R.56 Hydrophobic interactions: N:K.68 NAG-NAG-BMA-MAN-MAN-FUC.33: 7 residues within 4Å: Chain D: N.55, G.56, Y.57, T.58 Chain J: W.127, N.136, E.137 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.57 Hydrogen bonds: D:T.58

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(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-MAN-MAN.8: 13 residues within 4Å: Chain A: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain B: N.106, S.108, V.129, G.132, Y.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.232, A:C.231 NAG-NAG-BMA-MAN-MAN-MAN.19: 13 residues within 4Å: Chain E: 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, Y.134 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.232 NAG-NAG-BMA-MAN-MAN-MAN.30: 15 residues within 4Å: Chain I: G.197, D.229, H.230, C.231, Q.232, F.233, S.234, R.235, S.237 Chain J: N.106, S.108, V.129, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.232

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.10: 4 residues within 4Å: Chain A: Y.200 Chain B: N.131, G.132, S.133 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.21: 4 residues within 4Å: Chain E: Y.200, F.233 Chain F: N.131 Chain L: Q.62 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain E Hydrogen bonds: L:Q.62 Hydrophobic interactions: E:F.233 NAG-NAG-FUC.32: 2 residues within 4Å: Chain D: Q.65 Chain J: N.131 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.65

1 x NAG- NAG- BMA- MAN: 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.15: 7 residues within 4Å: Chain E: E.76, T.77, N.79, M.80, W.227 Chain F: W.24 Chain G: S.67 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.18: 2 residues within 4Å: Chain E: F.117, N.119 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., A cocktail of protective antibodies subverts the dense glycan shield of Lassa virus. Sci Transl Med (2022)

Release Date

2022-11-02

Peptides

Glycoprotein G1: AEI
Glycoprotein G2: BFJ
37.2D light chain (variable domain): CGK
37.2D heavy chain (variable domain): DHL
8.9F heavy chain (variable domain): M
8.9F light chain (variable domain): N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
B

I
C

B
a

F
b

J
c

C
T

G
P

K
R

D
S

H
O

L
Q

M
H

N
L

Glycoprotein G1

Glycoprotein G2

37.2D light chain (variable domain)

37.2D heavy chain (variable domain)

8.9F heavy chain (variable domain)

8.9F light chain (variable domain)

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