6WEY | pdb_00006wey

High-resolution structure of the SARS-CoV-2 NSP3 Macro X domain

• PDB DOI: https://doi.org/10.2210/pdb6WEY/pdb

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


• Deposited: 2020-04-03 Released: 2020-04-29 
• Deposition Author(s): Vuksanovic, N., Silvaggi, N.R.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.136 (Depositor), 0.139 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.121 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Starting Model: experimental

Literature

Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3.

Frick, D.N., Virdi, R.S., Vuksanovic, N., Dahal, N., Silvaggi, N.R.

(2020) Biochemistry 59: 2608-2615

• PubMed: 32578982 
• DOI: https://doi.org/10.1021/acs.biochem.0c00309
• Primary Citation Related Structures: 
  6WEY


• PubMed Abstract: 
  

  The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymerase, helicase, and main protease, are well conserved between SARS-CoV-2 and the original SARS virus, but several others are not. This study examines one of the proteins encoded by SARS-CoV-2 that is most different, a macrodomain of nonstructural protein 3 (nsp3). Although 26% of the amino acids in this SARS-CoV-2 macrodomain differ from those observed in other coronaviruses, biochemical and structural data reveal that the protein retains the ability to bind ADP-ribose, which is an important characteristic of beta coronaviruses and a potential therapeutic target.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.49 kDa 
• Atom Count: 1,831 
• Modeled Residue Count: 172 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A	172	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.136 (Depositor), 0.139 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.121 (DCC) 
• R-Value Observed: 0.120 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.322	α = 90
b = 54.424	β = 90
c = 67.567	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Vuksanovic, N., Silvaggi, N.R.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1903899

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2020-08-26
  Changes: Database references
• Version 1.3: 2020-09-02
  Changes: Source and taxonomy
• Version 1.4: 2021-01-27
  Changes: Structure summary
• Version 1.5: 2023-10-18
  Changes: Data collection, Database references, Refinement description