SMTL ID : 7uov.1

Native Lassa glycoprotein in complex with neutralizing antibodies 12.1F and 37.2D

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-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 C: E.76, T.77, N.79, M.80, N.99, W.227 Chain D: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain C: I.113, K.116, Q.165, N.167, S.169 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 7 residues within 4Å: Chain I: S.111, I.113, K.116, Q.165, N.167, S.169, Y.219 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:K.116 NAG-NAG-BMA.15: 7 residues within 4Å: Chain I: E.76, T.77, N.79, M.80, N.99, W.227 Chain J: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 6 residues within 4Å: Chain O: T.77, N.79, M.80, N.99, W.227 Chain P: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 7 residues within 4Å: Chain O: S.111, I.113, K.116, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP)

6 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.2: 15 residues within 4Å: Chain A: N.30, F.32, Y.99, Y.101, F.103, Y.108, Y.110, D.112 Chain B: Y.49, A.55, T.56 Chain C: K.88, N.89, S.91, H.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.110, A:D.112, A:Y.108, A:N.30 NAG-NAG-BMA-MAN-MAN-MAN.7: 14 residues within 4Å: Chain C: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain D: N.106, S.108, V.129, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.232, C:C.231 NAG-NAG-BMA-MAN-MAN-MAN.11: 15 residues within 4Å: Chain G: S.28, F.32, Y.99, Y.101, F.103, Y.108, Y.110, D.112 Chain H: Y.49, A.55, T.56 Chain I: K.88, N.89, S.91, H.92 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.99, G:Y.108, G:S.28, G:S.28 NAG-NAG-BMA-MAN-MAN-MAN.18: 12 residues within 4Å: Chain I: D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain J: N.106, S.108, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.232 NAG-NAG-BMA-MAN-MAN-MAN.24: 14 residues within 4Å: Chain M: E.27, S.28, Y.99, Y.101, F.103, Y.108, Y.110, D.112 Chain N: Y.49, T.56 Chain O: K.88, N.89, S.91, H.92 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:Y.110, M:Y.110, M:Y.108, M:E.27, M:S.28, M:S.28 NAG-NAG-BMA-MAN-MAN-MAN.29: 13 residues within 4Å: Chain O: D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain P: N.106, S.108, V.129, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:Q.232

2 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.3: 9 residues within 4Å: Chain A: F.103, A.104, W.105, N.107 Chain B: S.30 Chain C: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.22: 11 residues within 4Å: Chain M: A.104, W.105, N.107 Chain N: S.28, V.29, S.30, D.93 Chain O: N.109, S.216, Y.217, Q.218 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:S.30, N:S.30, N:D.93

7 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: 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.9: 3 residues within 4Å: Chain D: N.131 Chain L: R.59, Q.65 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Q.65 NAG-NAG-BMA-FUC.12: 9 residues within 4Å: Chain G: F.103, A.104, W.105, N.107 Chain H: S.30 Chain I: N.109, S.216, Y.217, Q.218 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:S.30, H:S.30 NAG-NAG-BMA-FUC.13: 3 residues within 4Å: Chain I: H.115, F.117, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.20: 2 residues within 4Å: Chain J: N.131 Chain Q: W.94 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:Q.65 NAG-NAG-BMA-FUC.26: 6 residues within 4Å: Chain O: H.115, F.117, N.119, D.122, D.156, N.158 2 PLIP interactions: 2 interactions with chain O Hydrophobic interactions: O:N.119, O:D.122 NAG-NAG-BMA-FUC.31: 3 residues within 4Å: Chain E: W.94 Chain F: R.59 Chain P: N.131 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.6: 4 residues within 4Å: Chain C: G.159, G.160, K.161, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 8 residues within 4Å: Chain C: Q.69 Chain D: E.30, K.32, C.33, F.34, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.30 NAG-NAG.16: 3 residues within 4Å: Chain I: N.99, E.100 Chain J: Q.72 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain I: G.159, G.160, K.161, N.224, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 7 residues within 4Å: Chain I: Q.69 Chain J: E.30, K.32, C.33, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:E.30 NAG-NAG.25: 3 residues within 4Å: Chain O: N.99, E.100 Chain P: Q.72 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain O: G.159, G.160, K.161, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 7 residues within 4Å: Chain P: K.32, C.33, F.34, Y.112, N.114, T.116, T.121 No protein-ligand interaction detected (PLIP)

3 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.10: 7 residues within 4Å: Chain C: T.59 Chain D: N.136, E.137 Chain L: N.55, G.56, Y.57, T.58 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain C Hydrophobic interactions: L:N.55, L:Y.57 Hydrogen bonds: C:T.59, C:T.59, L:T.58 NAG-NAG-BMA-MAN-MAN-FUC.21: 5 residues within 4Å: Chain J: N.136, E.137 Chain R: N.55, G.56, Y.57 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:N.55, R:T.58 NAG-NAG-BMA-MAN-MAN-FUC.32: 6 residues within 4Å: Chain F: N.55, G.56, Y.57, T.58 Chain P: N.136, E.137 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:N.55, F:Y.57 Hydrogen bonds: F:T.58

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

NAG.33: 3 residues within 4Å: Chain C: N.99, E.100 Chain D: Q.72 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.72, C:N.99, C:E.100

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

12.1F heavy chain (variable domain): AGM
12.1F light chain (variable domain): BHN
Glycoprotein G1: CIO
Glycoprotein G2: DJP
37.2D light chain (variable domain): EKQ
37.2D heavy chain (variable domain): FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

G
D

M
F

B
L

H
E

N
G

C
A

I
B

O
C

D
a

J
b

P
c

E
T

K
P

Q
R

F
S

L
O

R
Q

12.1F heavy chain (variable domain)

12.1F light chain (variable domain)

Glycoprotein G1

Glycoprotein G2

37.2D light chain (variable domain)

37.2D heavy chain (variable domain)

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