6O75

Crystal structure of Csm1-Csm4 cassette in complex with pppApA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path.

Jia, N.Jones, R.Sukenick, G.Patel, D.J.

(2019) Mol Cell 75: 933-943.e6

  • DOI: 10.1016/j.molcel.2019.06.013
  • Primary Citation of Related Structures:  
    6O79, 6O78, 6O73, 6O75, 6O74, 6O7I, 6O7H, 6O7B, 6O7E, 6O7D

  • PubMed Abstract: 
  • Target RNA binding to crRNA-bound type III-A CRISPR-Cas multi-subunit Csm surveillance complexes activates cyclic-oligoadenylate (cA n ) formation from ATP subunits positioned within the composite pair of Palm domain pockets of the Csm1 subunit ...

    Target RNA binding to crRNA-bound type III-A CRISPR-Cas multi-subunit Csm surveillance complexes activates cyclic-oligoadenylate (cA n ) formation from ATP subunits positioned within the composite pair of Palm domain pockets of the Csm1 subunit. The generated cA n second messenger in turn targets the CARF domain of trans-acting RNase Csm6, triggering its HEPN domain-based RNase activity. We have undertaken cryo-EM studies on multi-subunit Thermococcus onnurineus Csm effector ternary complexes, as well as X-ray studies on Csm1-Csm4 cassette, both bound to substrate (AMPPNP), intermediates (pppA n ), and products (cA n ), to decipher mechanistic aspects of cA n formation and release. A network of intermolecular hydrogen bond alignments accounts for the observed adenosine specificity, with ligand positioning dictating formation of linear pppA n intermediates and subsequent cA n formation by cyclization. We combine our structural results with published functional studies to highlight mechanistic insights into the role of the Csm effector complex in mediating the cA n signaling pathway.


    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
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)A791Thermococcus onnurineusMutation(s): 1 
Gene Names: csm1cas10TON_0893
EC: 3.1 (PDB Primary Data), 2.7.7 (PDB Primary Data)
UniProt
Find proteins for B6YWB8 (Thermococcus onnurineus (strain NA1))
Explore B6YWB8 
Go to UniProtKB:  B6YWB8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Csm4B289Thermococcus onnurineusMutation(s): 0 
Gene Names: TON_0896
UniProt
Find proteins for B6YWC1 (Thermococcus onnurineus (strain NA1))
Explore B6YWC1 
Go to UniProtKB:  B6YWC1
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-D(*(ATP))-R(P*A)-3')C, D2synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    E [auth A], F [auth A]MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.271 
    • R-Value Work: 0.223 
    • R-Value Observed: 0.226 
    • Space Group: P 65 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 156.445α = 90
    b = 156.445β = 90
    c = 186.415γ = 120
    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