8EQS: ORF3a protein

Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like environment, MSP1D1 nanodisc. Determined by electron microscopy at 3.1 Å resolution. Released 8 Feb 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Severe acute respiratory syndrome coronavirus, Homo sapiens
Chains: 4
Atoms: 3,654
Mol. weight: 123.43 kDa
Ligands: PEE
Released: 8 Feb 2023

Explore 8EQS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EQS contains 12 α-helices and 16 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and B: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	44-60	17
α-helix	68-99	32
α-helix	106-133	28
α-helix	137-140	4
β-strand	145-150	6	1
β-strand	155-160	6	1
β-strand	166-172	7	1
β-strand	183-186	4	1
β-strand	189-192	4	1
β-strand	200-204	5	1
β-strand	209-218	10	1
α-helix	220-223	4
β-strand	229-235	7	1

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	26-47	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ORF3a protein	A, B	protein	330	Severe acute respiratory syndrome coronavirus	P59632
Apolipoprotein A-I	C, D	protein	211	Homo sapiens	P02647 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8EQS_1 ORF3a protein (chains A, B)
MDLFMRFFTLGSITAQPVKIDNASPASTVHATATIPLQASLPFGWLVIGVAFLAVFQSAT
KIIALNKRWQLALYKGFQFICNLLLLFVTIYSHLLLVAAGMEAQFLYLYALIYFLQCINA
CRIIMRCWLCWKCKSKNPLLYDANYFVCWHTHNYDYCIPYNSVTDTIVVTEGDGISTPKL
KEDYQIGGYSEDRHSGVKDYVVVHGYFTEVYYQLESTQITTDTGIENATFFIFNKLVKDP
PNVQIHTIDGSSGVANPAMDPIYDEPTTTTSVPLGGRGLEVLFQGPGSGQLVGSGGLEGG
GGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Sequence of entity 2 (C, D), FASTA

>8EQS_2 Apolipoprotein A-I (chains C, D)
GHHHHHHHDYDIPTTENLYFQGSTFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEE
VKAKVQPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEEMRDRA
RAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALE
DLRQGLLPVLESFKVSFLSALEEYTKKLNTQ

Ligands and cofactors

ID	Name	Formula	Copies
PEE	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine	C41 H78 N O8 P	2

Primary citation

The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins. Miller, A.N., Houlihan, P.R., Matamala, E. et al. Elife (2023) 12. DOI 10.7554/eLife.84477 · PubMed

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