SMTL ID : 8ewf.1

CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: R.134, L.136, G.139, N.140, N.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.134, A:R.134, A:N.141 NAG.2: 4 residues within 4Å: Chain A: K.115, T.116, F.118 Chain B: N.259 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.115, B:N.259 NAG.3: 6 residues within 4Å: Chain C: N.89, S.91, V.93, M.153, P.155, V.157 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.155 Hydrogen bonds: C:N.89 NAG.4: 6 residues within 4Å: Chain C: E.200, R.202 Chain D: K.115, T.116, F.118 Chain E: N.259 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: E:N.259, C:E.200, C:R.202, D:K.115 NAG.5: 5 residues within 4Å: Chain D: R.134, L.136, G.139, N.140, N.141 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.134, D:R.134, D:N.141 NAG.6: 5 residues within 4Å: Chain F: R.134, L.136, G.139, N.140, N.141 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.134, F:R.134, F:N.141 NAG.7: 4 residues within 4Å: Chain F: K.115, T.116, F.118 Chain G: N.259 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:N.259, F:K.115 NAG.8: 5 residues within 4Å: Chain H: R.134, L.136, G.139, N.140, N.141 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:R.134, H:R.134, H:N.141 NAG.9: 4 residues within 4Å: Chain H: K.115, T.116, F.118 Chain I: N.259 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:N.259, H:K.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zimmerman, O. et al., Alternate domain repeat usage in an alphavirus entry receptor enables host species expansion. To Be Published

Release Date

2023-10-25

Peptides

E1 envelope protein: ADFH
Spike glycoprotein E2: BEGI
Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
G

F
K

H
O

B
C

E
I

G
M

I
Q

C
E

Membrane

We predict this structure to be a membrane protein.
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E1 envelope protein

Spike glycoprotein E2

Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8

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