4ILL

Recognition and Cleavage of a non-structured CRISPR RNA by its Processing Endoribonuclease Cas6

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6.

Shao, Y., Li, H.

(2013) Structure 21: 385-393

  • DOI: 10.1016/j.str.2013.01.010
  • Primary Citation of Related Structures:  
    4ILR, 4ILL, 4ILM

  • PubMed Abstract: 

    • Clustered regularly interspaced short palindromic repeats (CRISPRs) confer adaptive immunity to prokaryotes through a small RNA-mediated mechanism. Specific endoribonucleases are required by all CRISPR-bearing organisms to process CRISPR RNAs into sm ...

    Clustered regularly interspaced short palindromic repeats (CRISPRs) confer adaptive immunity to prokaryotes through a small RNA-mediated mechanism. Specific endoribonucleases are required by all CRISPR-bearing organisms to process CRISPR RNAs into small RNA that serve as guides for defensive effector complexes. The molecular mechanism of how the endoribonucleases process the class of CRISPR RNA containing no predicted secondary structural features remains largely elusive. Here, we report cocrystal structures of a processing endoribonuclease bound with a noncleavable RNA substrate and its product-like fragment derived from a nonpalindramic repeat. The enzyme stabilizes a short RNA stem-loop structure near the cleavage site and cleaves the phosphodiester bond using an active site comprised of arginine and lysine residues. The distinct RNA binding and cleavage mechanisms underline the diversity in CRISPR RNA processing.

    Organizational Affiliation: 

    Institute of Molecular Biophysics, Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas6 2A, B289Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: cas6b, SSO2004
EC: 3.1
Find proteins for Q97WV8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97WV8 
Go to UniProtKB:  Q97WV8
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*CP*UP*AP*AP*UP*CP*UP*AP*CP*UP*AP*UP*AP*GP*AP*AP*UP*UP*GP*AP*AP*AP*G)-3')C, R24N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.735α = 90
b = 68.542β = 119.12
c = 79.831γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-12-31 
  • Released Date: 2013-03-20 
    • Deposition Author(s): Shao, Y., Li, H.

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references