7N3K | pdb_00007n3k

Oridonin-bound SARS-CoV-2 Nsp9

PDB DOI: https://doi.org/10.2210/pdb7N3K/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-06-01 Released: 2021-10-27
Deposition Author(s): Littler, D.R., Gully, B.S., Rossjohn, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.285 (Depositor), 0.290 (DCC)
R-Value Work:
0.226 (Depositor), 0.233 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

A natural product compound inhibits coronaviral replication in vitro by binding to the conserved Nsp9 SARS-CoV-2 protein.

Littler, D.R., Liu, M., McAuley, J.L., Lowery, S.A., Illing, P.T., Gully, B.S., Purcell, A.W., Chandrashekaran, I.R., Perlman, S., Purcell, D.F.J., Quinn, R.J., Rossjohn, J.

(2021) J Biological Chem 297: 101362-101362

PubMed: 34756886 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2021.101362
Primary Citation Related Structures:
7N3K

PubMed Abstract:
The Nsp9 replicase is a conserved coronaviral protein that acts as an essential accessory component of the multi-subunit viral replication/transcription complex. Nsp9 is the predominant substrate for the essential nucleotidylation activity of Nsp12. Compounds specifically interfering with this viral activity would facilitate its study. Using a native mass-spectrometry-based approach to screen a natural product library for Nsp9 binders, we identified an ent-kaurane natural product, oridonin, capable of binding to purified SARS-CoV-2 Nsp9 with micromolar affinities. By determining the crystal structure of the Nsp9-oridonin complex, we showed that oridonin binds through a conserved site near Nsp9's C-terminal GxxxG-helix. In enzymatic assays, oridonin's binding to Nsp9 reduces its potential to act as substrate for Nsp12's Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain. We also showed using in vitro cellular assays oridonin, while cytotoxic at higher doses has broad antiviral activity, reducing viral titer following infection with either SARS-CoV-2 or, to a lesser extent, MERS-CoV. Accordingly, these preliminary findings suggest that the oridonin molecular scaffold may have the potential to be developed into an antiviral compound to inhibit the function of Nsp9 during coronaviral replication.

Organizational Affiliation

Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. Electronic address: dene.littler@monash.edu.

Macromolecule Content

Total Structure Weight: 120.06 kDa
Atom Count: 7,785
Modeled Residue Count: 989
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 9	A, B, C, D, E A, B, C, D, E, F, G, H	133	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ODN (Subject of Investigation/LOI) Query on ODN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain R [auth G] SDF format, chain T [auth H] SDF format, chain P [auth F] SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain R [auth G] MOL2 format, chain T [auth H] MOL2 format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain R [auth G] mmCIF format, chain T [auth H] mmCIF format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain I [auth A]	I [auth A] J [auth B] L [auth C] M [auth D] O [auth E] I [auth A], J [auth B], L [auth C], M [auth D], O [auth E], P [auth F], R [auth G], T [auth H]	(1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one C₂₀ H₃₀ O₆ RWELMBQGCLVKOE-ZJOCIWLNSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain R [auth G] Focus chain T [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain R [auth G] Focus chain T [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain S [auth G] SDF format, chain N [auth D] SDF format, chain K [auth B] MOL2 format, chain Q [auth F] MOL2 format, chain S [auth G] MOL2 format, chain N [auth D] MOL2 format, chain K [auth B] mmCIF format, chain Q [auth F] mmCIF format, chain S [auth G] mmCIF format, chain N [auth D] mmCIF format, chain K [auth B]	K [auth B], N [auth D], Q [auth F], S [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Focus chain N [auth D] Focus chain Q [auth F] Focus chain S [auth G] Interactions & Density Focus chain K [auth B] Focus chain N [auth D] Focus chain Q [auth F] Focus chain S [auth G]