Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 243.14 kDa 
• Atom Count: 16484 
• Modelled Residue Count: 2027 
• Deposited Residue Count: 2060 
• Unique protein chains: 1

4IC1

Crystal structure of SSO0001

• PDB DOI: 10.2210/pdb4IC1/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-09 Released: 2013-01-16 
• Deposition Author(s): Nocek, B., Skarina, T., Lemak, S., Beloglazova, N., Flick, R., Brown, G., Savchenko, A., Joachimiak, A., Yakunin, A.F., Midwest Center for Structural Genomics (MCSG)

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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 

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

• PubMed: 24171432 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K]	206	Saccharolobus solfataricus P2	Mutation(s): 0  Gene Names: SSO0001, cas4 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	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
MN	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
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.249 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 
• Space Group: P 1 2₁ 1
• Diffraction Data DOI: 10.18430/M34IC1 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.152	α = 90
b = 197.761	β = 100.88
c = 89.41	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
Auto-Rickshaw	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-09 
• Released Date: 2013-01-16 
Deposition Author(s): Nocek, B., Skarina, T., Lemak, S., Beloglazova, N., Flick, R., Brown, G., Savchenko, A., Joachimiak, A., Yakunin, A.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

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