8EQU: ORF3a protein

Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A nanodisc. Determined by electron microscopy at 2.8 Å resolution. Released 8 Feb 2023.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 8
Atoms: 5,764
Mol. weight: 124.79 kDa
Ligands: PEE
Released: 8 Feb 2023

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

Secondary structure: helices and β-sheets

8EQU contains 36 α-helices and 16 β-strands across 8 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	44-60	17
α-helix	68-98	31
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
β-strand	228-235	8	1

Chains C and F: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	2-18	17
α-helix	21-36	16
α-helix	43-46	4
α-helix	47-51	5
α-helix	52-66	15
α-helix	69-75	7

Chains D, E, G and H: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	2-18	17
α-helix	21-35	15
α-helix	41-66	26
α-helix	69-75	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ORF3a protein	A, B	protein	331	Severe acute respiratory syndrome coronavirus 2	P0DTC3 (AlphaFold model)
Saposin-A	C, F	protein	106	Homo sapiens	P07602 (AlphaFold model)
Saposin A, polyalanine model	D, E, G, H	protein	79	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>8EQU_1 ORF3a protein (chains A, B)
MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSAS
KIITLKKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGLEAPFLYLYALVYFLQSINF
VRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPIS
EHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEP
EEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPLGGRGLEVLFQGPGSGQLVGSGGLEG
GGGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Sequence of entity 2 (C, F), FASTA

>8EQU_2 Saposin-A (chains C, F)
MGGHHHHHHSSGVDLGTENLYFQSMSLPCDICKDVVTAAGDMLKDNATEEEILVYLEKTC
DWLPKPNMSASCKEIVDSYLPVILDIIKGEMSRPGEVCSALNLCES

Sequence of entity 3 (D, E, G, H), FASTA

>8EQU_3 Saposin A, polyalanine model (chains D, E, G, H)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXX

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

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
7KJR 2.08 Å, Cryo-EM structure of SARS-CoV-2 ORF3a
8T5P 2.5 Å, SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain
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

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