SMTL ID : 7puy.1

Structure of the membrane soluble spike complex from the Lassa virus in a C3-symmetric map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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.1: 3 residues within 4Å: Chain D: H.115, N.119, D.156 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain D: K.116, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: W.24 Chain D: E.76, T.77, N.79, N.99, W.227 Ligands: NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain E: H.115, N.119, D.156 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain E: K.116, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain B: W.24 Chain E: E.76, T.77, N.79, N.99, W.227 Ligands: NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain F: H.115, N.119, D.156 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain F: K.116, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain C: W.24 Chain F: E.76, T.77, N.79, N.99, W.227 Ligands: NAG.26 No protein-ligand interaction detected (PLIP)

3 x XYS- BDP- XYS: alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose

XYS-BDP-XYS.4: 5 residues within 4Å: Chain D: R.256, R.257, L.258 Chain E: Y.150 Chain F: S.121 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:R.257, D:R.257, D:L.258, D:R.256, D:R.256, F:S.121 Salt bridges: D:R.256, D:R.257 XYS-BDP-XYS.8: 5 residues within 4Å: Chain D: S.121 Chain E: R.256, R.257, L.258 Chain F: Y.150 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.257, E:R.257, E:L.258, D:S.121, E:R.256, E:R.256 Salt bridges: E:R.256, E:R.257 XYS-BDP-XYS.12: 5 residues within 4Å: Chain D: Y.150 Chain E: S.121 Chain F: R.256, R.257, L.258 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.257, F:R.257, F:L.258, E:S.121, F:R.256, F:R.256 Salt bridges: F:R.256, F:R.257

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

NAG.13: 6 residues within 4Å: Chain A: N.106, Y.134 Chain D: W.196, F.233, S.234, R.235 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain A: K.32, Y.112, N.114, T.116, T.121 Chain D: Q.69 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.136, H.139 Ligand excluded by PLIP NAG.16: 6 residues within 4Å: Chain B: N.106, Y.134 Chain E: W.196, F.233, S.234, R.235 Ligand excluded by PLIP NAG.17: 6 residues within 4Å: Chain B: K.32, Y.112, N.114, T.116, T.121 Chain E: Q.69 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.136, H.139 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain C: N.106, Y.134 Chain F: W.196, F.233, S.234, R.235 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain C: K.32, Y.112, N.114, T.116, T.121 Chain F: Q.69 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: N.136, H.139 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain D: M.80, N.99 Ligands: NAG-NAG.3, NAG-NAG.3 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: N.109, S.216, Y.217 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain E: M.80, N.99 Ligands: NAG-NAG.7, NAG-NAG.7 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain E: N.109, S.216, Y.217 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain F: M.80, N.99 Ligands: NAG-NAG.11, NAG-NAG.11 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain F: N.109, S.216, Y.217 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katz, M. et al., Structure and receptor recognition by the Lassa virus spike complex. Nature (2022)

Release Date

2021-12-29

Peptides

Glycoprotein G2: ABC
Pre-glycoprotein polyprotein GP complex: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
b

C
c

D
A

E
B

F
C

Membrane

We predict this structure to be a membrane protein.
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Glycoprotein G2

Pre-glycoprotein polyprotein GP complex

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