6W02 | pdb_00006w02

Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose

• PDB DOI: https://doi.org/10.2210/pdb6W02/pdb

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


• Deposited: 2020-02-28 Released: 2020-03-11 
• Deposition Author(s): Michalska, K., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Mesecar, A., 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: 1.50 Å
• R-Value Free: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

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 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: 
• Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.
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: 37.73 kDa 
• Atom Count: 3,016 
• Modeled Residue Count: 332 
• 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
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APR (Subject of Investigation/LOI)	C [auth A], E [auth B]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36w02

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.264	α = 97.859
b = 37.842	β = 97.377
c = 68.296	γ = 89.941

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-11 
Deposition Author(s): Michalska, K., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Mesecar, A., 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: 2020-03-11
  Type: Initial release
  
• Version 2.0: 2020-04-22
  Changes: Advisory, Atomic model, Data collection, 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
• Version 2.6: 2023-10-11
  Changes: Data collection, Refinement description