6O6Y

Crystal structure of Csm6 in complex with cyclic-tetraadenylates (cA4) by cocrystallization of Csm6 and cA4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 

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:  

  • 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 <sub>n </sub>) from ATP and subsequent cA <sub>n </sub>-mediated ...

    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

    Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: jian@mskcc.org.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: pateld@mskcc.org.,Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Csm6
A, B
440Thermococcus onnurineus (strain NA1)Mutation(s): 0 
Find proteins for B6YWC3 (Thermococcus onnurineus (strain NA1))
Go to UniProtKB:  B6YWC3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACK
Query on ACK

Download SDF File 
Download CCD File 
A, B
2',3'- cyclic AMP
C10 H12 N5 O6 P
KMYWVDDIPVNLME-KQYNXXCUSA-N
 Ligand Interaction
LQJ
Query on LQJ

Download SDF File 
Download CCD File 
A, B
3'-O-[(R)-{[(2S,3aS,4S,6S,6aS)-6-(6-amino-9H-purin-9-yl)-2-hydroxy-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]adenosine
C20 H24 N10 O12 P2
ZKDCIJKZCQKMKS-RJLGOGMOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 103.451α = 90.00
b = 163.963β = 90.00
c = 111.105γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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