4D2I | pdb_00004d2i

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

PDB DOI: https://doi.org/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 (Depositor), 0.252 (DCC)
R-Value Work:
0.211 (Depositor), 0.217 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/ncomms6506
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 112.86 kDa
Atom Count: 7,462
Modeled Residue Count: 922
Deposited Residue Count: 1,000
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HERA	A, B	500	Saccharolobus solfataricus P2	Mutation(s): 10 EC: 5.6.2.4 (UniProt), 5.6.2.3 (UniProt)
UniProt
Find proteins for Q97WG8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97WG8 Go to UniProtKB: Q97WG8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97WG8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.254 (Depositor), 0.252 (DCC)
R-Value Work: 0.211 (Depositor), 0.217 (DCC)
R-Value Observed: 0.213 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-12-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-03
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other