7TWV | pdb_00007twv

Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 5 (P43 crystal form)

• PDB DOI: https://doi.org/10.2210/pdb7TWV/pdb

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


• Deposited: 2022-02-07 Released: 2022-02-23 
• Deposition Author(s): Correy, G.J., Fraser, J.S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free: 
  0.107 (Depositor), 0.106 (DCC) 
• R-Value Work: 
  0.095 (Depositor), 0.095 (DCC) 
• R-Value Observed: 
  0.096 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 5 (P43 crystal form)

Correy, G.J., Fraser, J.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.3 kDa 
• Atom Count: 3,563 
• Modeled Residue Count: 336 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B	169	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
AR6 (Subject of Investigation/LOI)	C [auth A]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N
CIT	D [auth A], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free:  0.107 (Depositor), 0.106 (DCC) 
• R-Value Work:  0.095 (Depositor), 0.095 (DCC) 
• R-Value Observed: 0.096 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.393	α = 90
b = 88.393	β = 90
c = 39.924	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): Correy, G.J., Fraser, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	GM123159
National Science Foundation (NSF, United States)	United States	2031205

Revision History  

• Version 1.0: 2022-02-23
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description