1Z63

Sulfolobus solfataricus SWI2/SNF2 ATPase core in complex with dsDNA

• PDB DOI: https://doi.org/10.2210/pdb1Z63/pdb
• NAKB: 1Z63

• Classification: HYDROLASE/DNA complex
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-03-21 Released: 2005-05-17 
• Deposition Author(s): Duerr, H., Koerner, C., Mueller, M., Hickmann, V., Hopfner, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.281 
• R-Value Work: 0.233 
• R-Value Observed: 0.233 

Literature

X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA.

Durr, H., Korner, C., Muller, M., Hickmann, V., Hopfner, K.P.

(2005) Cell 121: 363-373

• PubMed: 15882619 
• DOI: https://doi.org/10.1016/j.cell.2005.03.026
• Primary Citation of Related Structures:  
  1Z5Z, 1Z63, 1Z6A


• PubMed Abstract: 
  

  SWI2/SNF2 ATPases remodel chromatin or other DNA:protein complexes by a poorly understood mechanism that involves ATP-dependent DNA translocation and generation of superhelical torsion. Crystal structures of a dsDNA-translocating SWI2/SNF2 ATPase core from Sulfolobus solfataricus reveal two helical SWI2/SNF2 specific subdomains, fused to a DExx box helicase-related ATPase core. Fully base paired duplex DNA binds along a central cleft via both minor groove strands, indicating that SWI2/SNF2 ATPases travel along the dsDNA minor groove without strand separation. A structural switch, linking DNA binding and the active site DExx motif, may account for the stimulation of ATPase activity by dsDNA. Our results suggest that torque in remodeling processes is generated by an ATP-driven screw motion of DNA along the active site cleft. The structures also redefine SWI2/SNF2 functional motifs and uncover unexpected structural correlation of mutations in Cockayne and X-linked mental retardation syndromes.

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Organizational Affiliation: 

Gene Center and Department of Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 145.92 kDa 
• Atom Count: 9,154 
• Modelled Residue Count: 1,014 
• Deposited Residue Count: 1,100 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase of the snf2/rad54 family	E [auth A], F [auth B]	500	Saccharolobus solfataricus	Mutation(s): 0
UniProt
Find proteins for Q97XQ7 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97XQ7  Go to UniProtKB:  Q97XQ7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*AP*AP*AP*A*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP*AP*AP*AP*A)-3'	A [auth C], C [auth E]	25	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*TP*TP*TP*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*TP*TP*TP*TP*TP*T)-3'	B [auth D], D [auth F]	25	N/A

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	E [auth A], F [auth B]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.281 
• R-Value Work: 0.233 
• R-Value Observed: 0.233 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.931	α = 90
b = 83.737	β = 109.78
c = 106.39	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
XDS	data reduction
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-17 
Deposition Author(s): Duerr, H., Koerner, C., Mueller, M., Hickmann, V., Hopfner, K.P.

Revision History  

• Version 1.0: 2005-05-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-04-16
  Changes: Experimental preparation
• Version 1.4: 2017-08-23
  Changes: Advisory, Refinement description, Source and taxonomy
• Version 1.5: 2024-11-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary