6W01 | pdb_00006w01

The 1.9 A Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate

• PDB DOI: https://doi.org/10.2210/pdb6W01/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): Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, 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: 1.90 Å
• R-Value Free: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2.

Kim, Y., Jedrzejczak, R., Maltseva, N.I., Wilamowski, M., Endres, M., Godzik, A., Michalska, K., Joachimiak, A.

(2020) Protein Sci 29: 1596-1605

• PubMed: 32304108 
• DOI: https://doi.org/10.1002/pro.3873
• Primary Citation Related Structures: 
  6VWW, 6W01


• PubMed Abstract: 
  

  Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is rapidly spreading around the world. There is no existing vaccine or proven drug to prevent infections and stop virus proliferation. Although this virus is similar to human and animal SARS-CoVs and Middle East Respiratory Syndrome coronavirus (MERS-CoVs), the detailed information about SARS-CoV-2 proteins structures and functions is urgently needed to rapidly develop effective vaccines, antibodies, and antivirals. We applied high-throughput protein production and structure determination pipeline at the Center for Structural Genomics of Infectious Diseases to produce SARS-CoV-2 proteins and structures. Here we report two high-resolution crystal structures of endoribonuclease Nsp15/NendoU. We compare these structures with previously reported homologs from SARS and MERS coronaviruses.

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Organizational Affiliation: 
• Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
Biomedical Sciences, University of California Riverside, Riverside, California, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 85.38 kDa 
• Atom Count: 6,253 
• Modeled Residue Count: 694 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate-specific endoribonuclease	A, B	370	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.1
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
CIT	N [auth A], X [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
PEG	AA [auth B], G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	BA [auth B], C [auth A], CA [auth B], D [auth A], E [auth A], F [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36w01

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.784	α = 90
b = 150.784	β = 90
c = 111.682	γ = 120

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): Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, 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: 2020-03-11
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 2.0: 2020-06-10
  Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2020-07-08
  Changes: Database references
• Version 2.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description