Crystal Structure of ADP ribose phosphatase of NSP3 from SARS-CoV-2 in the apo form

Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.106 

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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

  • 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.

  • Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 3170Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.671α = 90
b = 29.677β = 103.52
c = 37.886γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Source and taxonomy
  • Version 1.2: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2020-09-30
    Changes: Database references
  • Version 1.4: 2020-10-14
    Changes: Source and taxonomy, Structure summary
  • Version 1.5: 2021-01-27
    Changes: Structure summary
  • Version 1.6: 2023-10-18
    Changes: Data collection, Database references, Refinement description