6O6X

Crystal structure of Csm6 W14A/E337A mutant in complex with cA4 by cocrystallization

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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:  
    6O6S, 6O6T, 6O6V, 6O6X, 6O6Y, 6O6Z, 6O70, 6O71, 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

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Csm6A, B440Thermococcus onnurineusMutation(s): 2 
Gene Names: TON_0898
UniProt
Find proteins for B6YWC3 (Thermococcus onnurineus (strain NA1))
Explore B6YWC3 
Go to UniProtKB:  B6YWC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YWC3
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
Cyclic RNA cA4C, D 4synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.148α = 90
b = 115.745β = 90
c = 161.037γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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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