7KJR: SARS-CoV-2 ORF3a

Cryo-EM structure of SARS-CoV-2 ORF3a. Determined by electron microscopy at 2.08 Å resolution. Released 18 Nov 2020.

Method: Electron microscopy
Resolution: 2.08 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 4
Atoms: 3,840
Mol. weight: 115.12 kDa
Ligands: PEE
Released: 18 Nov 2020

Explore 7KJR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KJR contains 16 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.

Chain A: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	44-60	17
α-helix	68-99	32
α-helix	103-105	3
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	228-235	8	1
α-helix	236	1

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	44-60	17
α-helix	68-99	32
α-helix	103-133	31
α-helix	137-140	4
β-strand	145-150	6	2
β-strand	155-160	6	2
β-strand	166-172	7	2
β-strand	183-186	4	2
β-strand	189-192	4	2
β-strand	200-204	5	2
β-strand	209-218	10	2
α-helix	220-223	4
β-strand	228-235	8	2
α-helix	236-237	2

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	26-54	29

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	26-46	21
α-helix	48-54	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ORF3a protein	A, B	protein	284	Severe acute respiratory syndrome coronavirus 2	P0DTC3 (AlphaFold model)
Apolipoprotein A-I	C, D	protein	210	Homo sapiens	P02647 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7KJR_1 ORF3a protein (chains A, B)
MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSAS
KIITLKKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGLEAPFLYLYALVYFLQSINF
VRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPIS
EHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEP
EEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPLSNSLEVLFQ

Sequence of entity 2 (C, D), FASTA

>7KJR_2 Apolipoprotein A-I (chains C, D)
HHHHHHHDYDIPTTENLYFQGSTFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEV
KAKVQPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEEMRDRAR
AHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALED
LRQGLLPVLESFKVSFLSALEEYTKKLNTQ

Ligands and cofactors

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

Primary citation

Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs. Kern, D.M., Sorum, B., Mali, S.S. et al. Nat Struct Mol Biol (2021) 28:573-582. DOI 10.1038/s41594-021-00619-0 · PubMed

Other PDB entries of the same protein (UniProt P0DTC3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8T5Q 1.9 Å, SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain
8T5P 2.5 Å, SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain
8EQU 2.8 Å, Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A…
6XDC 2.9 Å, Cryo-EM structure of SARS-CoV-2 ORF3a
8EQJ 3.0 Å, Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like membrane environment,…
9RU5 3.26 Å, Cryo-EM structure of TCRpub/pMHC
8EQT 3.4 Å, Structure of SARS-CoV-2 Orf3a in plasma membrane-like environment, MSP1D1 nanodisc

Browse structure collections

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