4ILM | pdb_00004ilm

CRISPR RNA Processing endoribonuclease

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 
    0.284 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 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: https://doi.org/10.1016/j.str.2013.01.010
  • Primary Citation Related Structures: 
    4ILL, 4ILM, 4ILR

  • 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 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

Macromolecule Content 

  • Total Structure Weight: 302.01 kDa 
  • Atom Count: 20,435 
  • Modeled Residue Count: 2,353 
  • Deposited Residue Count: 2,440 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas6 2289Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: cas6b, SSO2004
EC: 3.1
UniProt
Find proteins for Q97WV8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97WV8 
Go to UniProtKB:  Q97WV8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97WV8
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*CP*UP*AP*AP*UP*CP*UP*AP*CP*UP*AP*UP*AP*GP*A)-3')16N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free:  0.284 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.981α = 90
b = 154.608β = 93.64
c = 130.848γ = 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

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references