7KRI | pdb_00007kri

FR6-bound SARS-CoV-2 Nsp9 RNA-replicase

• PDB DOI: https://doi.org/10.2210/pdb7KRI/pdb

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


• Deposited: 2020-11-20 Released: 2021-07-21 
• Deposition Author(s): Littler, D.R., Gully, B.S., Rossjohn, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 nonstructural protein 9.

Littler, D.R., Mohanty, B., Lowery, S.A., Colson, R.N., Gully, B.S., Perlman, S., Scanlon, M.J., Rossjohn, J.

(2021) J Biological Chem 297: 101018-101018

• PubMed: 34331944 
• DOI: https://doi.org/10.1016/j.jbc.2021.101018
• Primary Citation Related Structures: 
  7KRI


• PubMed Abstract: 
  

  The coronaviral nonstructural protein 9 (Nsp9) is essential for viral replication; it is the primary substrate of Nsp12's pseudokinase domain within the viral replication transcription complex, an association that also recruits other components during different stages of RNA reproduction. In the unmodified state, Nsp9 forms an obligate homodimer via an essential GxxxG protein-interaction motif, but its ssRNA-binding mechanism remains unknown. Using structural biological techniques, here we show that a base-mimicking compound identified from a small molecule fragment screen engages Nsp9 via a tetrameric Pi-Pi stacking interaction that induces the formation of a parallel trimer-of-dimers. This oligomerization mechanism allows an interchange of "latching" N-termini, the charges of which contribute to a series of electropositive channels that suggests a potential interface for viral RNA. The identified pyrrolo-pyrimidine compound may also serve as a potential starting point for the development of compounds seeking to probe Nsp9's role within SARS-CoV-2 replication.

---

Organizational Affiliation: 
• Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. Electronic address: [e-mail].
Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; Sydney Analytical Core Research Facility, The University of Sydney, Sydney, New South Wales, Australia; ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA.
Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia. Electronic address: [e-mail].
Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 45.24 kDa 
• Atom Count: 3,307 
• Modeled Residue Count: 377 
• Deposited Residue Count: 399 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 9	A, B, C	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X0Y (Subject of Investigation/LOI)	E [auth A], F [auth A], H [auth B], I [auth B], L [auth C], M [auth C]	1,3-dimethyl-1H-pyrrolo[3,4-d]pyrimidine-2,4(3H,6H)-dione C8 H9 N3 O2 MNPOFAXKBZPGNK-UHFFFAOYSA-N
MLI	K [auth C]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
SO4	D [auth A], G [auth B], J [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.459	α = 90
b = 109.459	β = 90
c = 77.046	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Littler, D.R., Gully, B.S., Rossjohn, J.

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2021-08-04
  Changes: Database references
• Version 1.2: 2021-08-25
  Changes: Database references
• Version 1.3: 2021-09-01
  Changes: Database references
• Version 1.4: 2023-10-18
  Changes: Data collection, Refinement description