3ZFV | pdb_00003zfv

Crystal structure of an archaeal CRISPR-associated Cas6 nuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.236 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3ZFV

This is version 1.3 of the entry. See complete history

Literature

Structure of a Dimeric Crenarchaeal Cas6 Enzyme with an Atypical Active Site for Crispr RNA Processing

Reeks, J.Sokolowski, R.Graham, S.Liu, H.Naismith, J.H.White, M.F.

(2013) Biochem J 452: 223

  • DOI: https://doi.org/10.1042/BJ20130269
  • Primary Citation Related Structures: 
    3ZFV

  • PubMed Abstract: 

    The competition between viruses and hosts is played out in all branches of life. Many prokaryotes have an adaptive immune system termed 'CRISPR' (clustered regularly interspaced short palindromic repeats) which is based on the capture of short pieces of viral DNA. The captured DNA is integrated into the genomic DNA of the organism flanked by direct repeats, transcribed and processed to generate crRNA (CRISPR RNA) that is loaded into a variety of effector complexes. These complexes carry out sequence-specific detection and destruction of invading mobile genetic elements. In the present paper, we report the structure and activity of a Cas6 (CRISPR-associated 6) enzyme (Sso1437) from Sulfolobus solfataricus responsible for the generation of unit-length crRNA species. The crystal structure reveals an unusual dimeric organization that is important for the enzyme's activity. In addition, the active site lacks the canonical catalytic histidine residue that has been viewed as an essential feature of the Cas6 family. Although several residues contribute towards catalysis, none is absolutely essential. Coupled with the very low catalytic rate constants of the Cas6 family and the plasticity of the active site, this suggests that the crRNA recognition and chaperone-like activities of the Cas6 family should be considered as equal to or even more important than their role as traditional enzymes.


  • Organizational Affiliation
    • Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.

Macromolecule Content 

  • Total Structure Weight: 132.75 kDa 
  • Atom Count: 8,191 
  • Modeled Residue Count: 1,027 
  • Deposited Residue Count: 1,172 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1
A, B, C, D
293Saccharolobus solfataricusMutation(s): 0 
EC: 3.1
UniProt
Find proteins for Q97Y96 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97Y96 
Go to UniProtKB:  Q97Y96
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97Y96
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.236 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.65α = 90
b = 127.46β = 110.48
c = 83.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references
  • Version 1.2: 2013-05-29
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary