6O6V

Crystal structure of Csm6 in complex with cA4 by soaking cA4 into Csm6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

CRISPR-Cas III-A Csm6 CARF Domain Is a Ring Nuclease Triggering Stepwise cA4Cleavage with ApA>p Formation Terminating RNase Activity.

Jia, N.Jones, R.Yang, G.Ouerfelli, O.Patel, D.J.

(2019) Mol Cell 75: 944-956.e6

  • DOI: 10.1016/j.molcel.2019.06.014
  • Primary Citation of Related Structures:  
    6O6V, 6O6X, 6O6Z, 6O6Y, 6O71, 6O70, 6O6T, 6O6S, 6OV0

  • PubMed Abstract: 
  • Type III-A CRISPR-Cas surveillance complexes containing multi-subunit Csm effector, guide, and target RNAs exhibit multiple activities, including formation of cyclic-oligoadenylates (cA n ) from ATP and subsequent cA n -mediated cleavage of single-strand RNA (ssRNA) by the trans-acting Csm6 RNase ...

    Type III-A CRISPR-Cas surveillance complexes containing multi-subunit Csm effector, guide, and target RNAs exhibit multiple activities, including formation of cyclic-oligoadenylates (cA n ) from ATP and subsequent cA n -mediated cleavage of single-strand RNA (ssRNA) by the trans-acting Csm6 RNase. Our structure-function studies have focused on Thermococcus onnurineus Csm6 to deduce mechanistic insights into how cA 4 binding to the Csm6 CARF domain triggers the RNase activity of the Csm6 HEPN domain and what factors contribute to regulation of RNA cleavage activity. We demonstrate that the Csm6 CARF domain is a ring nuclease, whereby bound cA 4 is stepwise cleaved initially to ApApApA>p and subsequently to ApA>p in its CARF domain-binding pocket, with such cleavage bursts using a timer mechanism to regulate the RNase activity of the Csm6 HEPN domain. In addition, we establish T. onnurineus Csm6 as an adenosine-specific RNase and identify a histidine in the cA 4 CARF-binding pocket involved in autoinhibitory regulation of RNase activity.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: pateld@mskcc.org.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Csm6A, B440Thermococcus onnurineusMutation(s): 0 
Gene Names: TON_0898
UniProt
Find proteins for B6YWC3 (Thermococcus onnurineus (strain NA1))
Explore B6YWC3 
Go to UniProtKB:  B6YWC3
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    Cyclic RNA cA4C, D4synthetic construct
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.35 Å
    • R-Value Free: 0.271 
    • R-Value Work: 0.227 
    • R-Value Observed: 0.229 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 103.993α = 90
    b = 164.414β = 90
    c = 111.324γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2019-03-07 
    • Released Date: 2019-07-31 
    • Deposition Author(s): Jia, N., Patel, D.J.

    Revision History  (Full details and data files)

    • Version 1.0: 2019-07-31
      Type: Initial release
    • Version 1.1: 2019-09-18
      Changes: Data collection, Database references