4IC1 | pdb_00004ic1

Crystal structure of SSO0001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4IC1

This is version 1.2 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: https://doi.org/10.1021/ja408729b
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 243.14 kDa 
  • Atom Count: 16,484 
  • Modeled Residue Count: 2,027 
  • Deposited Residue Count: 2,060 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein206Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: SSO0001
EC: 3.1.12.1
UniProt
Find proteins for Q97TX9 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97TX9 
Go to UniProtKB:  Q97TX9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97TX9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / 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]
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-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
AA [auth J]
CA [auth K]
K [auth A]
M [auth B]
O [auth C]
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
B
C
D
E [auth F]
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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 1 21 1
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 

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
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary