7K9P

Room temperature structure of NSP15 Endoribonuclease from SARS CoV-2 solved using SFX.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser.

Jernigan, R.J.Logeswaran, D.Doppler, D.Nagaratnam, N.Sonker, M.Yang, J.H.Ketawala, G.Martin-Garcia, J.M.Shelby, M.L.Grant, T.D.Mariani, V.Tolstikova, A.Sheikh, M.Z.Yung, M.C.Coleman, M.A.Zaare, S.Kaschner, E.K.Rabbani, M.T.Nazari, R.Zacks, M.A.Hayes, B.Sierra, R.G.Hunter, M.S.Lisova, S.Batyuk, A.Kupitz, C.Boutet, S.Hansen, D.T.Kirian, R.A.Schmidt, M.Fromme, R.Frank, M.Ros, A.Chen, J.J.Botha, S.Fromme, P.

(2022) Structure 

  • DOI: https://doi.org/10.1016/j.str.2022.12.009
  • Primary Citation of Related Structures:  
    7K9P

  • PubMed Abstract: 

    NendoU from SARS-CoV-2 is responsible for the virus's ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.


  • Organizational Affiliation

    Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridylate-specific endoribonuclease
A, B
349Severe 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154α = 90
b = 154β = 90
c = 117γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF2031343
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM095583
National Science Foundation (NSF, United States)United States1231306

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description