8JBC

Crystal Structure of the Csm6 K137A mutant from Thermus thermophilus HB8 in its apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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

Molecular mechanism of allosteric activation of the CRISPR ribonuclease Csm6 by cyclic tetra-adenylate.

Du, L.Zhu, Q.Lin, Z.

(2024) EMBO J 43: 304-315

  • DOI: https://doi.org/10.1038/s44318-023-00017-w
  • Primary Citation of Related Structures:  
    8JBB, 8JBC, 8JH1

  • PubMed Abstract: 

    Type III CRISPR systems are innate immune systems found in bacteria and archaea, which produce cyclic oligoadenylate (cOA) second messengers in response to viral infections. In these systems, Csm6 proteins serve as ancillary nucleases that degrade single-stranded RNA (ssRNA) upon activation by cOA. In addition, Csm6 proteins also possess cOA-degrading activity as an intrinsic off-switch to avoid degradation of host RNA and DNA that would eventually lead to cell dormancy or cell death. Here, we present the crystal structures of Thermus thermophilus (Tt) Csm6 alone, and in complex with cyclic tetra-adenylate (cA 4 ) in both pre- and post-cleavage states. These structures establish the molecular basis of the long-range allosteric activation of TtCsm6 ribonuclease by cA 4 . cA 4 binding induces significant conformational changes, including closure of the CARF domain, dimerization of the HTH domain, and reorganization of the R-X 4-6 -H motif within the HEPN domain. The cleavage of cA 4 by the CARF domain restores each domain to a conformation similar to its apo state. Furthermore, we have identified hyperactive TtCsm6 variants that exhibit sustained cA 4 -activated RNase activity, showing great promise for their applications in genome editing and diagnostics.


  • Organizational Affiliation

    College of Chemistry, Fuzhou University, 350108, Fuzhou, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system endoribonuclease Csm6
A, B
468Thermus thermophilus HB8Mutation(s): 1 
Gene Names: csm6TTHB152
EC: 3.1
UniProt
Find proteins for Q53W17 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q53W17 
Go to UniProtKB:  Q53W17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53W17
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.89α = 90
b = 205.57β = 90
c = 59.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing
PHENIXmodel building
Cootmodel building
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2023-12-13 
  • Deposition Author(s): Lin, Z., Du, L.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971222

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Database references