6XDC: SARS-CoV-2 ORF3a

Cryo-EM structure of SARS-CoV-2 ORF3a. Determined by electron microscopy at 2.9 Å resolution. Released 17 Jun 2020.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 2
Atoms: 3,150
Mol. weight: 64.33 kDa
Released: 17 Jun 2020

Explore 6XDC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XDC contains 10 α-helices and 20 β-strands across 2 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: 5 helices, 10 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	145-148	4	1
β-strand	150	1	2
β-strand	155	1	2
β-strand	158-160	3	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

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	44-60	17
α-helix	68-99	32
α-helix	103-132	30
α-helix	137-140	4
β-strand	145-148	4	3
β-strand	150	1	4
β-strand	155	1	4
β-strand	158-160	3	3
β-strand	166-172	7	3
β-strand	183-186	4	3
β-strand	189-192	4	3
β-strand	200-204	5	3
β-strand	209-218	10	3
α-helix	220-223	4
β-strand	228-235	8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ORF3a protein	A, B	protein	284	Severe acute respiratory syndrome coronavirus 2	P0DTC3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6XDC_1 ORF3a protein (chains A, B)
MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSAS
KIITLKKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGLEAPFLYLYALVYFLQSINF
VRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPIS
EHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEP
EEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPLSNSLEVLFQ

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
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
8EQU 2.8 Å, Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A…
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 more

6XDC is part of these collections:

SARS-CoV-2 and COVID-19

About this viewer

MolViewer shows 6XDC directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.