Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 84.38 kDa 
• Atom Count: 6009 
• Residue Count: 696 
• Unique protein chains: 1

6VWW

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2.

• DOI: 10.2210/pdb6VWW/pdb

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


• Deposited: 2020-02-20 Released: 2020-03-04 
• 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: 2.20 Å
• R-Value Free: 0.178 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 

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: 10.1002/pro.3873
• Primary Citation of 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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Related Citations: 

• Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2.
  Kim, Y., Jedrzejczak, R., Maltseva, N.I., Endres, M., Godzik, A., Michalska, K., Joachimiak, A.
  (2020) Biorxiv --: --

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.

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 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (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), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	A, B	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.178 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 
• Space Group: P 6₃
• Diffraction Data DOI: 10.18430/m36vww Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.539	α = 90
b = 150.539	β = 90
c = 111.31	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-02-20 
• Released Date: 2020-03-04 
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: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2020-03-11
  Changes: Database references, Source and taxonomy
• Version 1.2: 2020-04-01
  Changes: Data collection
• Version 1.3: 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