7K1O

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-3',5'-Diphosphate

• PDB DOI: https://doi.org/10.2210/pdb7K1O/pdb

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


• Deposited: 2020-09-08 Released: 2020-09-23 
• Deposition Author(s): Kim, Y., Maltseva, N., Jedrzejczak, R., Endres, M., Welk, L., Chang, C., 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: 2.40 Å
• R-Value Free: 0.242 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-3',5'-Diphosphate

Kim, Y., Maltseva, N., Jedrzejczak, R., Endres, M., Welk, L., Chang, C., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 126.37 kDa 
• Atom Count: 8,386 
• Modelled Residue Count: 1,040 
• Deposited Residue Count: 1,110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate-specific endoribonuclease	A, B, C	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VQV (Subject of Investigation/LOI)	D [auth A], F [auth B], H [auth C]	1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione C9 H14 N2 O12 P2 ZPVPRWPOZBXDKD-ZAKLUEHWSA-N
EDO	E [auth A], G [auth B], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.242 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/m37k1o

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.46	α = 90
b = 151.321	β = 90
c = 197.518	γ = 90

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

• Released Date: 2020-09-23 
Deposition Author(s): Kim, Y., Maltseva, N., Jedrzejczak, R., Endres, M., Welk, L., Chang, C., 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: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description