SMTL ID : 8d87.1

Fitted crystal structure of the homotrimer of fusion glycoprotein E1 from SFV into subtomogram averaged CHIKV E1 glycoprotein density

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 27.20 Å

Oligo State

homo-trimer

Ligands

1 x NAG- NAG- BMA- BMA- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-NAG-FUL.1: 4 residues within 4Å: Chain A: Q.32, R.134, M.136, N.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.32

1 x NDG- NAG- BMA- MAN- NAG- MAN- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-NAG-BMA-MAN-NAG-MAN-FUC.2: 3 residues within 4Å: Chain B: R.134, M.136, N.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.134, B:N.141 Water bridges: B:R.134

1 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 C: M.136, N.141 No protein-ligand interaction detected (PLIP)

3 x BR: BROMIDE ION(Non-covalent)

BR.4: 1 residues within 4Å: Chain A: P.191 Ligand excluded by PLIP BR.8: 1 residues within 4Å: Chain B: K.123 Ligand excluded by PLIP BR.10: 1 residues within 4Å: Chain C: P.191 Ligand excluded by PLIP

4 x HO: HOLMIUM ATOM(Covalent)(Non-covalent)

HO.5: 6 residues within 4Å: Chain A: K.176, D.188 Chain B: K.176, D.188 Chain C: K.176, D.188 Ligand excluded by PLIP HO.6: 3 residues within 4Å: Chain A: Y.390, A.391 Chain C: E.72 Ligand excluded by PLIP HO.9: 3 residues within 4Å: Chain A: E.72 Chain B: Y.390, A.391 Ligand excluded by PLIP HO.11: 3 residues within 4Å: Chain B: E.72 Chain C: Y.390, A.391 Ligand excluded by PLIP

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 5 residues within 4Å: Chain A: S.168 Chain B: S.168, A.169 Chain C: S.168, A.169 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:S.168, B:A.169, A:S.168, C:S.168, C:S.168, C:A.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mangala Prasad, V. et al., Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery. Nat Commun (2022)

Release Date

2022-08-31

Peptides

Spike glycoprotein E1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein E1

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