SMTL ID : 6zqv.1

Cryo-EM structure of mature Spondweni virus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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.1: 7 residues within 4Å: Chain A: H.148, G.150, M.151, N.154, T.156, N.157, D.161 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.161 NAG-NAG-FUC.2: 7 residues within 4Å: Chain C: H.148, G.150, M.151, N.154, T.156, N.157, D.161 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:D.161 NAG-NAG-FUC.3: 7 residues within 4Å: Chain E: H.148, G.150, M.151, N.154, T.156, N.157, D.161 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:D.161 Hydrogen bonds: E:D.161

3 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.4: 12 residues within 4Å: Chain A: M.422, A.423, V.424, G.426, V.446, H.447, F.450, F.454, M.495, F.498 Chain B: L.12, E.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.422, A:V.446, A:F.450, A:F.498 Hydrogen bonds: A:A.423 Salt bridges: A:H.447 3PE.5: 13 residues within 4Å: Chain C: A.419, M.422, A.423, V.424, G.426, V.446, H.447, G.451, F.454, M.495, L.499 Chain D: L.12, E.13 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:M.422, C:V.446 Hydrogen bonds: C:A.423, C:G.451 3PE.6: 13 residues within 4Å: Chain E: A.423, V.424, G.426, W.430, V.446, H.447, F.450, F.454, M.495, F.498, L.499 Chain F: L.12, E.13 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:A.423, E:W.430, E:V.446, E:H.447, E:F.450, E:F.498 Hydrogen bonds: E:A.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Renner, M. et al., Flavivirus maturation leads to the formation of an occupied lipid pocket in the surface glycoproteins. Nat Commun (2021)

Release Date

2021-01-20

Peptides

Genome polyprotein: ACE
Genome polyprotein: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Genome polyprotein

Genome polyprotein

Related Entries With Identical Sequence