Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 112.86 kDa 
• Atom Count: 7462 
• Residue Count: 922 
• Unique protein chains: 1

4D2I

Crystal structure of the HerA hexameric DNA translocase from Sulfolobus solfataricus bound to AMP-PNP

• DOI: 10.2210/pdb4D2I/pdb

• Classification: HYDROLASE
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-05-09 Released: 2014-12-03 
• Deposition Author(s): Rzechorzek, N.J., Blackwood, J.K., Bray, S.M., Maman, J.D., Pellegrini, L., Robinson, N.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.254 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

Structure of the Hexameric Hera ATPase Reveals a Mechanism of Translocation-Coupled DNA-End Processing in Archaea

Rzechorzek, N.J., Blackwood, J.K., Bray, S.M., Maman, J.D., Pellegrini, L., Robinson, N.P.

(2014) Nat Commun 5: 5506

• PubMed: 25420454 
• DOI: 10.1038/ncomms6506
• Primary Citation of Related Structures:  
  4D2I


• PubMed Abstract: 
  

The HerA ATPase cooperates with the NurA nuclease and the Mre11-Rad50 complex for the repair of double-strand DNA breaks in thermophilic archaea. Here we extend our structural knowledge of this minimal end-resection apparatus by presenting the first crystal structure of hexameric HerA. The full-length structure visualizes at atomic resolution the N-terminal HerA-ATP synthase domain and a conserved C-terminal extension, which acts as a physical brace between adjacent protomers. The brace also interacts in trans with nucleotide-binding residues of the neighbouring subunit. Our observations support a model in which the coaxial interaction of the HerA ring with the toroidal NurA dimer generates a continuous channel traversing the complex. HerA-driven translocation would propel the DNA towards the narrow annulus of NurA, leading to duplex melting and nucleolytic digestion. This system differs substantially from the bacterial end-resection paradigms. Our findings suggest a novel mode of DNA-end processing by this integrated archaeal helicase-nuclease machine.

---

Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HERA	A, B	500	Saccharolobus solfataricus P2	Mutation(s): 10  Gene Names: herA, SSO2251 EC: 3.6.4.12
Find proteins for Q97WG8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97WG8  Go to UniProtKB:  Q97WG8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	A, B	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.254 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.21	α = 90
b = 150.21	β = 90
c = 140.54	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-09 
• Released Date: 2014-12-03 
Deposition Author(s): Rzechorzek, N.J., Blackwood, J.K., Bray, S.M., Maman, J.D., Pellegrini, L., Robinson, N.P.

Revision History 

• Version 1.0: 2014-12-03
  Type: Initial release