SMTL ID : 8sqn.1

CryoEM structure of Western equine encephalitis virus VLP in complex with the chimeric Du-D1-Mo-D2 MXRA8 receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-4-4-mer

Ligands

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.1: 9 residues within 4Å: Chain A: N.89, S.91, V.93, M.153, V.157, R.159 Chain B: G.83, S.98, K.223 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.89, A:V.157 Hydrogen bonds: A:N.89, A:R.159 NAG.2: 2 residues within 4Å: Chain B: N.139, H.327 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain C: N.195, S.211, T.212 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.212 NAG.4: 3 residues within 4Å: Chain D: G.138, N.139, H.327 No protein-ligand interaction detected (PLIP) NAG.5: 4 residues within 4Å: Chain E: N.195, S.211, T.212, R.230 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:T.212 NAG.6: 4 residues within 4Å: Chain A: K.128 Chain F: G.138, N.139, H.327 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain G: N.195, S.211, T.212, R.230 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:T.212 Hydrogen bonds: G:R.230 NAG.8: 3 residues within 4Å: Chain H: G.138, N.139, H.327 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:H.327 NAG.9: 4 residues within 4Å: Chain I: N.195, S.211, T.212, R.230 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:T.212 Hydrogen bonds: I:S.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zimmerman, O. et al., Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8. Cell (2023)

Release Date

2023-12-20

Peptides

DuD1MoD2 chimeric MXRA8: A
E1 envelope glycoprotein: BDFH
E2 envelope glycoprotein: CEGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
F

F
J

H
N

C
D

E
H

G
L

I
P

Membrane

We predict this structure to be a membrane protein.
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DuD1MoD2 chimeric MXRA8

E1 envelope glycoprotein

E2 envelope glycoprotein

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