4IC1

Crystal structure of SSO0001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus.

Lemak, S.Beloglazova, N.Nocek, B.Skarina, T.Flick, R.Brown, G.Popovic, A.Joachimiak, A.Savchenko, A.Yakunin, A.F.

(2013) J Am Chem Soc 135: 17476-17487

  • DOI: 10.1021/ja408729b
  • Primary Citation of Related Structures:  
    4IC1

  • PubMed Abstract: 
  • Cas4 proteins, a core protein family associated with the microbial system of adaptive immunity CRISPR, are predicted to function in the adaptation step of the CRISPR mechanism. Here we show that the Cas4 protein SSO0001 from the archaeon Sulfolobus solfataricus has metal-dependent endonuclease and 5'→3' exonuclease activities against single-stranded DNA, as well as ATP-independent DNA unwinding activity toward double-stranded DNA ...

    Cas4 proteins, a core protein family associated with the microbial system of adaptive immunity CRISPR, are predicted to function in the adaptation step of the CRISPR mechanism. Here we show that the Cas4 protein SSO0001 from the archaeon Sulfolobus solfataricus has metal-dependent endonuclease and 5'→3' exonuclease activities against single-stranded DNA, as well as ATP-independent DNA unwinding activity toward double-stranded DNA. The crystal structure of SSO0001 revealed a decameric toroid formed by five dimers with each protomer containing one [4Fe-4S] cluster and one Mn(2+) ion bound in the active site located inside the internal tunnel. The conserved RecB motif and four Cys residues are important for DNA binding and cleavage activities, whereas DNA unwinding depends on several residues located near the [4Fe-4S] cluster. Our results suggest that Cas4 proteins might contribute to the addition of novel CRISPR spacers through the formation of 3'-DNA overhangs and to the degradation of foreign DNA.


    Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto, Ontario M5S 3E5, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein206Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: SSO0001cas4
EC: 3.1.12.1
Find proteins for Q97TX9 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97TX9 
Go to UniProtKB:  Q97TX9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
BA [auth J] , DA [auth K] , L [auth A] , N [auth B] , P [auth C] , R [auth D] , T [auth F] , V [auth G] , 
BA [auth J],  DA [auth K],  L [auth A],  N [auth B],  P [auth C],  R [auth D],  T [auth F],  V [auth G],  X [auth H],  Z [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth J] , CA [auth K] , K [auth A] , M [auth B] , O [auth C] , Q [auth D] , S [auth F] , U [auth G] , 
AA [auth J],  CA [auth K],  K [auth A],  M [auth B],  O [auth C],  Q [auth D],  S [auth F],  U [auth G],  W [auth H],  Y [auth I]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A , B , C , D , E [auth F] , F [auth G] , G [auth H] , H [auth I] , 
A,  B,  C,  D,  E [auth F],  F [auth G],  G [auth H],  H [auth I],  I [auth J],  J [auth K]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.152α = 90
b = 197.761β = 100.88
c = 89.41γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
Auto-Rickshawphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references