SMTL ID : 8eqj.1

Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like membrane environment, MSP1D1 nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

PEE.1: 9 residues within 4Å: Chain A: I.118, V.121, R.122, R.126, N.144, Y.206 Chain B: I.62, I.63, T.64 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.121, B:I.62 Salt bridges: A:R.122 Hydrogen bonds: B:I.63, B:T.64 PEE.2: 7 residues within 4Å: Chain A: K.75, G.76, H.78, F.79, R.122, I.123, L.140 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.140 Hydrogen bonds: A:N.82, A:R.122 PEE.3: 9 residues within 4Å: Chain A: I.62, I.63, T.64 Chain B: I.118, V.121, R.122, R.126, N.144, Y.206 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.62, B:V.121 Hydrogen bonds: A:I.63, A:T.64 Salt bridges: B:R.122 PEE.4: 7 residues within 4Å: Chain B: K.75, G.76, H.78, F.79, R.122, I.123, L.140 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.140 Hydrogen bonds: B:N.82, B:R.122

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

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

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