SMTL ID : 7v4t.1 (2 other biounits)

Cryo-EM structure of Alphavirus M1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: Q.30, R.134, N.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.141 NAG.2: 4 residues within 4Å: Chain A: F.95 Chain B: N.200, C.201, T.202 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.95 NAG.3: 3 residues within 4Å: Chain A: H.116 Chain B: T.261, N.262 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.261 Hydrogen bonds: B:N.262 NAG.4: 2 residues within 4Å: Chain D: R.134, N.141 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.134, D:N.141 NAG.5: 4 residues within 4Å: Chain D: F.95 Chain E: N.200, C.201, T.202 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.95 NAG.6: 4 residues within 4Å: Chain D: H.116 Chain E: L.260, T.261, N.262 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:N.262, D:H.116, D:H.116 NAG.7: 2 residues within 4Å: Chain G: R.134, N.141 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.134, G:R.134, G:N.141 NAG.8: 5 residues within 4Å: Chain G: F.95 Chain H: N.200, C.201, T.202, N.207 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:N.207 Hydrophobic interactions: G:F.95 NAG.9: 4 residues within 4Å: Chain G: H.116 Chain H: L.260, T.261, N.262 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:H.116, H:N.262 NAG.10: 3 residues within 4Å: Chain J: Q.30, R.134, N.141 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.134, J:N.141 NAG.11: 4 residues within 4Å: Chain J: F.95 Chain K: N.200, C.201, T.202 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: J:F.95, K:T.202 NAG.12: 4 residues within 4Å: Chain J: H.116 Chain K: L.260, T.261, N.262 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:H.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, D. et al., Cryo-EM evidence of viral N-glycosylation reveal receptor binding mechanisms of alphavirus M1. To Be Published

Release Date

2022-08-17

Peptides

E1 glycoprotein: ADGJ
E2 glycoprotein: BEHK
Capsid protein: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

G
I

J
M

B
B

E
F

H
J

K
N

C
C

F
G

I
K

L
O

E1 glycoprotein

E2 glycoprotein

Capsid protein

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