6O74

Crystal structure of Csm1-Csm4 cassette in complex with AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 

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:  

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

    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: jian@mskcc.org.,Chemical Biology Program Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,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: pateld@mskcc.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Csm4
B
289Thermococcus onnurineus (strain NA1)Mutation(s): 0 
Gene Names: csm4
Find proteins for B6YWC1 (Thermococcus onnurineus (strain NA1))
Go to UniProtKB:  B6YWC1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Csm1
A
791Thermococcus onnurineus (strain NA1)Mutation(s): 0 
Gene Names: csm1 (cas10)
EC: 3.1.-.-
Find proteins for B6YWB8 (Thermococcus onnurineus (strain NA1))
Go to UniProtKB:  B6YWB8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 156.432α = 90.00
b = 156.432β = 90.00
c = 185.473γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement

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