SMTL ID : 8p4t.1

The spike complex of the Lujo Virus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 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.1: 3 residues within 4Å: Chain A: N.54, T.56, R.57 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.4: 3 residues within 4Å: Chain D: N.54, T.56, R.57 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.6: 3 residues within 4Å: Chain E: N.54, T.56, R.57 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-(1-6)-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.2: 3 residues within 4Å: Chain A: N.90, S.92, Y.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 3 residues within 4Å: Chain D: N.90, S.92, Y.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.7: 3 residues within 4Å: Chain E: N.90, S.92, Y.93 No protein-ligand interaction detected (PLIP)

3 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: 6 residues within 4Å: Chain B: I.31, F.34, Y.112, N.114, H.121 Chain D: E.10 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain E: E.10 Chain H: I.31, F.34, Y.112, N.114, H.121 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain A: E.10 Chain I: I.31, F.34, Y.112, N.114, H.121 No protein-ligand interaction detected (PLIP)

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

NAG.10: 5 residues within 4Å: Chain A: N.15, S.17, L.18 Chain I: E.22, I.26 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: T.45, N.46 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: H.36, D.134, N.136 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain A: S.21, N.35, H.36 Chain I: I.64, R.68, A.71 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.131 Ligand excluded by PLIP NAG.16: 6 residues within 4Å: Chain B: N.106, T.108, V.129, G.132, Y.134 Chain D: H.141 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.136 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain B: E.22, I.26 Chain D: N.15, S.17, L.18 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain D: T.45, N.46 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: H.36, D.134, N.136 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain B: I.64, R.68, A.71 Chain D: S.21, N.35, H.36 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain E: N.15, S.17, L.18 Chain H: E.22, I.26 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain E: T.45, N.46 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain E: H.36, D.134, N.136 Ligand excluded by PLIP NAG.25: 6 residues within 4Å: Chain E: S.21, N.35, H.36 Chain H: I.64, R.68, A.71 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain H: N.131 Ligand excluded by PLIP NAG.27: 7 residues within 4Å: Chain E: E.27, H.141 Chain H: N.106, T.108, V.129, G.132, Y.134 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain H: N.136 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain I: N.131 Ligand excluded by PLIP NAG.30: 7 residues within 4Å: Chain A: E.27, H.141 Chain I: N.106, T.108, V.129, G.132, Y.134 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain I: N.136 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.14: 3 residues within 4Å: Chain A: E.154 Chain D: E.154 Chain E: E.154 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eilon-Ashkenazy, M. et al., The structure of the Lujo virus spike complex. Nat Commun (2024)

Release Date

2024-06-12

Peptides

Glycoprotein: ADE
Glycoprotein: BHI
Glycoprotein: CFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

E
C

B
a

H
b

I
c

C
SA

F
SB

G
SC

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Glycoprotein

Glycoprotein

Glycoprotein