3PKM | pdb_00003pkm

Crystal structure of Cas6 with its substrate RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.318 (Depositor), 0.340 (DCC) 
  • R-Value Work: 
    0.276 (Depositor), 0.301 (DCC) 
  • R-Value Observed: 
    0.308 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Interaction of the Cas6 Riboendonuclease with CRISPR RNAs: Recognition and Cleavage.

Wang, R.Preamplume, G.Terns, M.P.Terns, R.M.Li, H.

(2011) Structure 19: 257-264

  • DOI: https://doi.org/10.1016/j.str.2010.11.014
  • Primary Citation Related Structures: 
    3PKM

  • PubMed Abstract: 

    The CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) found in prokaryotic genomes confer small RNA-mediated protection against viruses and other invaders. CRISPR loci contain iterations of a short repeat sequence alternating with small segments of varying invader-derived sequences. Distinct families of CRISPR-associated Cas proteins function to cleave within the repeat sequence of CRISPR transcripts and produce the individual invader-targeting crRNAs. Here, we report the crystal structure of Pyrococcus furiosus Cas6 bound with a repeat RNA at 3.2 Å resolution. In contrast to other Cas families of endonucleases, Cas6 clasps nucleotides 2-9 of the repeat RNA using its two ferredoxin-like domains, and the enzyme-anchored 5' end tethers the distal cleavage site of the RNA between nucleotides 22 and 23 to the predicted enzyme active site on the opposite side of the ferrodoxin-like domains. Our findings suggest a wrap-around mechanism for CRISPR RNA recognition and cleavage by Cas6 and related processing endonucleases.


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

Macromolecule Content 

  • Total Structure Weight: 68.61 kDa 
  • Atom Count: 4,195 
  • Modeled Residue Count: 480 
  • Deposited Residue Count: 557 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas6A,
B [auth X]
269Pyrococcus furiosusMutation(s): 0 
Gene Names: cas6PF1131
EC: 3.1
UniProt
Find proteins for Q8U1S4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U1S4 
Go to UniProtKB:  Q8U1S4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U1S4
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(*AP*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'C [auth G]10synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
5'-R(P*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'D [auth R]9synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.318 (Depositor), 0.340 (DCC) 
  • R-Value Work:  0.276 (Depositor), 0.301 (DCC) 
  • R-Value Observed: 0.308 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.557α = 90
b = 96.557β = 90
c = 165.492γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
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: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Source and taxonomy, Structure summary