7N33

SARS-CoV-2 Nsp15 endoribonuclease pre-cleavage state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U.

Frazier, M.N.Dillard, L.B.Krahn, J.M.Perera, L.Williams, J.G.Wilson, I.M.Stewart, Z.D.Pillon, M.C.Deterding, L.J.Borgnia, M.J.Stanley, R.E.

(2021) Nucleic Acids Res 49: 10136-10149

  • DOI: https://doi.org/10.1093/nar/gkab719
  • Primary Citation of Related Structures:  
    7N06, 7N33

  • PubMed Abstract: 

    Nsp15 is a uridine specific endoribonuclease that coronaviruses employ to cleave viral RNA and evade host immune defense systems. Previous structures of Nsp15 from across Coronaviridae revealed that Nsp15 assembles into a homo-hexamer and has a conserved active site similar to RNase A. Beyond a preference for cleaving RNA 3' of uridines, it is unknown if Nsp15 has any additional substrate preferences. Here, we used cryo-EM to capture structures of Nsp15 bound to RNA in pre- and post-cleavage states. The structures along with molecular dynamics and biochemical assays revealed critical residues involved in substrate specificity, nuclease activity, and oligomerization. Moreover, we determined how the sequence of the RNA substrate dictates cleavage and found that outside of polyU tracts, Nsp15 has a strong preference for purines 3' of the cleaved uridine. This work advances our understanding of how Nsp15 recognizes and processes viral RNA, and will aid in the development of new anti-viral therapeutics.


  • Organizational Affiliation

    Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.


Macromolecules

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
360Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.1
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*A)-D(*(UFT))-R(P*A)-3')
G, H, I, J, K
G, H, I, J, K, L
3Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIA ES103247
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZ01 ES043010
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZI CES102488
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZI CES103206
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIC ES103326
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1ZIAES103340

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-09-01
    Changes: Database references
  • Version 1.2: 2021-10-06
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Data collection