7XMN: SARS-CoV-2 ORF8

Structure of SARS-CoV-2 ORF8. Determined by X-ray diffraction at 2.3 Å resolution. Released 31 May 2023.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Escherichia coli, Severe acute respiratory syndrome coronavirus 2
Chains: 2
Atoms: 3,824
Mol. weight: 53.89 kDa
Ligands: NAG, NNH
Released: 31 May 2023

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

Secondary structure: helices and β-sheets

7XMN contains 26 α-helices and 32 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: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	15-18	4	1
α-helix	25-39	15
β-strand	43-46	4	1
α-helix	51-60	10
β-strand	67-71	5	1
α-helix	72-74	3
α-helix	75-80	6
β-strand	84	1	2
α-helix	91-94	4
β-strand	97	1	3
α-helix	99-104	6
β-strand	106-107	2	4
β-strand	110-111	2	4
β-strand	114-119	6	1
β-strand	122-126	5	5
β-strand	136	1	6
α-helix	137-139	3
α-helix	140-148	9
β-strand	153-155	3	5
α-helix	162-171	10
β-strand	175-180	6	7
β-strand	183-190	8	7
α-helix	194-208	15
α-helix	218-226	9
β-strand	230-235	6	5
α-helix	237-239	3
α-helix	240-244	5
β-strand	250-253	4	5
α-helix	254-256	3
β-strand	257	1	6
β-strand	258	1	8
β-strand	261	1	8
α-helix	262-263	2
α-helix	265	1
β-strand	266-267	2	9
β-strand	268-274	7	1
β-strand	275	1	2
α-helix	281-287	7
α-helix	288-292	5
α-helix	295-304	10
β-strand	309-310	2	1
β-strand	312	1	3
α-helix	313-319	7
α-helix	323-333	11
β-strand	336-337	2	9
α-helix	338-339	2
α-helix	344-359	16
α-helix	365-376	12

Chain B: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	10
β-strand	30-32	3	11
α-helix	38	1
β-strand	41-49	9	10
α-helix	56	1
β-strand	57-59	3	10
β-strand	80-83	4	11
β-strand	86-89	4	11
β-strand	96-104	9	10
β-strand	107-120	14	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltodextrin-binding protein	A	protein	370	Escherichia coli	P0AEX9 (AlphaFold model)
ORF8 protein	B	protein	106	Severe acute respiratory syndrome coronavirus 2	P0DTC8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7XMN_1 Maltodextrin-binding protein (chains A)
KTEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDII
FWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKD
LLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKD
VGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEHAFNHGETAMTINGPWAWSNIDTSAV
NYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLG
AVALKSYEEELVKDPRVAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAA
LAAAQTNAAA

Sequence of entity 2 (B), FASTA

>7XMN_2 ORF8 protein (chains B)
FHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIELCVDEAGSKSPIQYID
IGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDFI

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
NNH	Nor-N-omega-hydroxy-L-arginine	C5 H12 N4 O3	1

Water and common crystallization additives (MES, SO4) are not listed.

Primary citation

Glycosylated, Lipid-Binding, CDR-Like Domains of SARS-CoV-2 ORF8 Indicate Unique Sites of Immune Regulation. Wu, F., Chen, X., Ma, Y. et al. Microbiol Spectr (2023) 11:e0123423-e0123423. DOI 10.1128/spectrum.01234-23 · PubMed

Other PDB entries of the same protein (UniProt P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

Browse structure collections

About this viewer

MolViewer shows 7XMN 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.