SMTL ID : 8eqs.1

Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like environment, MSP1D1 nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.1: 12 residues within 4Å: Chain A: I.118, R.122, Y.206, F.207 Chain B: I.62, I.63, A.64, Y.74 Chain D: L.32, T.36, F.39, W.40 10 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: D:L.32, D:L.32, D:F.39, A:I.118, A:I.118, A:R.122 Salt bridges: A:R.122 Hydrogen bonds: B:L.65, B:Y.74, B:Y.74 PEE.2: 12 residues within 4Å: Chain A: I.62, I.63, A.64, Y.74 Chain B: I.118, R.122, Y.206, F.207 Chain C: L.32, T.36, F.39, W.40 10 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:I.118, B:I.118, B:R.122, C:L.32, C:L.32, C:F.39 Salt bridges: B:R.122 Hydrogen bonds: A:L.65, A:Y.74, A:Y.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, A.N. et al., The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins. Elife (2023)

Release Date

2023-02-08

Peptides

ORF3a protein: AB
Apolipoprotein A-I: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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ORF3a protein

Apolipoprotein A-I