6O7D

Crystal structure of Csm1-Csm4 cassette in complex with one ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 onnurineus NA1Mutation(s): 0 
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 onnurineus NA1Mutation(s): 0 
Gene Names: TON_0896csm4
UniProt
Find proteins for B6YWC1 (Thermococcus onnurineus (strain NA1))
Explore B6YWC1 
Go to UniProtKB:  B6YWC1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MN
Query on MN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.255 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.776α = 90
b = 156.776β = 90
c = 185.767γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



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