6VXS

Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2

• PDB DOI:  https://doi.org/10.2210/pdb6VXS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-24 Released: 2020-03-04 
• Deposition Author(s): Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Mesecar, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.234 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes.

Michalska, K., Kim, Y., Jedrzejczak, R., Maltseva, N.I., Stols, L., Endres, M., Joachimiak, A.

(2020) IUCrJ 7: 814-824

• PubMed: 32939273 
• DOI: https://doi.org/10.1107/S2052252520009653
• Primary Citation of Related Structures:  
  6VXS, 6W02, 6W6Y, 6WCF, 6WEN


• PubMed Abstract: 
  

Among 15 nonstructural proteins (Nsps), the newly emerging Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) encodes a large, multidomain Nsp3. One of its units is the ADP-ribose phosphatase domain (ADRP; also known as the macrodomain, MacroD), which is believed to interfere with the host immune response. Such a function appears to be linked to the ability of the protein to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remain unknown. Here, five high-resolution (1.07-2.01 Å) crystal structures corresponding to the apo form of the protein and its complexes with 2-( N -morpholino)ethanesulfonic acid (MES), AMP and ADP-ribose have been determined. The protein is shown to undergo conformational changes to adapt to the ligand in the manner previously observed in close homologues from other viruses. A conserved water molecule is also identified that may participate in hydrolysis. This work builds foundations for future structure-based research on ADRP, including the search for potential antiviral therapeutics.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.41 kDa 
• Atom Count: 2,715 
• Modelled Residue Count: 334 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B	170	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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
NHE	D [auth A], H [auth B]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
SO4	C [auth A], E [auth A], F [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.234 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/m36vxs

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.391	α = 84.368
b = 37.896	β = 82.11
c = 65.4	γ = 90.114

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Mesecar, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Source and taxonomy
• Version 2.0: 2020-04-22
  Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 2.2: 2020-09-30
  Changes: Database references
• Version 2.3: 2020-10-14
  Changes: Source and taxonomy, Structure summary
• Version 2.4: 2021-01-27
  Changes: Structure summary
• Version 2.5: 2021-08-18
  Changes: Database references, Structure summary