Crystal structure of Nsp15-H234A mutant- Hexamer in asymmetric unit

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Structural and functional analyses of the severe acute respiratory syndrome coronavirus endoribonuclease Nsp15.

Bhardwaj, K.Palaninathan, S.Alcantara, J.M.Yi, L.L.Guarino, L.Sacchettini, J.C.Kao, C.C.

(2008) J Biol Chem 283: 3655-3664

  • DOI: https://doi.org/10.1074/jbc.M708375200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The severe acute respiratory syndrome (SARS) coronavirus encodes several RNA-processing enzymes that are unusual for RNA viruses, including Nsp15 (nonstructural protein 15), a hexameric endoribonuclease that preferentially cleaves 3' of uridines. We solved the structure of a catalytically inactive mutant version of Nsp15, which was crystallized as a hexamer. The structure contains unreported flexibility in the active site of each subunit. Substitutions in the active site residues serine 293 and proline 343 allowed Nsp15 to cleave at cytidylate, whereas mutation of leucine 345 rendered Nsp15 able to cleave at purines as well as pyrimidines. Mutations that targeted the residues involved in subunit interactions generally resulted in the formation of catalytically inactive monomers. The RNA-binding residues were mapped by a method linking reversible cross-linking, RNA affinity purification, and peptide fingerprinting. Alanine substitution of several residues in the RNA-contacting portion of Nsp15 did not affect hexamer formation but decreased the affinity of RNA binding and reduced endonuclease activity. This suggests a model for Nsp15 hexamer interaction with RNA.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas 77843-2128.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridylate-specific endoribonuclease
A, B, C, D, E
A, B, C, D, E, F
353Severe acute respiratory syndrome-related coronavirusMutation(s): 1 
Gene Names: NSP15
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 305.757α = 90
b = 305.757β = 90
c = 88.74γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description