6S16

T. thermophilus RuvC in complex with Holliday junction substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.409 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution.

Gorecka, K.M.Krepl, M.Szlachcic, A.Poznanski, J.Sponer, J.Nowotny, M.

(2019) Nat Commun 10: 4102-4102

  • DOI: 10.1038/s41467-019-11900-8

  • PubMed Abstract: 
  • Holliday junctions (HJs) are four-way DNA structures that occur in DNA repair by homologous recombination. Specialized nucleases, termed resolvases, remove (i.e., resolve) HJs. The bacterial protein RuvC is a canonical resolvase that introduces two s ...

    Holliday junctions (HJs) are four-way DNA structures that occur in DNA repair by homologous recombination. Specialized nucleases, termed resolvases, remove (i.e., resolve) HJs. The bacterial protein RuvC is a canonical resolvase that introduces two symmetric cuts into the HJ. For complete resolution of the HJ, the two cuts need to be tightly coordinated. They are also specific for cognate DNA sequences. Using a combination of structural biology, biochemistry, and a computational approach, here we show that correct positioning of the substrate for cleavage requires conformational changes within the bound DNA. These changes involve rare high-energy states with protein-assisted base flipping that are readily accessible for the cognate DNA sequence but not for non-cognate sequences. These conformational changes and the relief of protein-induced structural tension of the DNA facilitate coordination between the two cuts. The unique DNA cleavage mechanism of RuvC demonstrates the importance of high-energy conformational states in nucleic acid readouts.


    Organizational Affiliation

    Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65, Brno, Czech Republic.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109, Warsaw, Poland.,Institute of Biochemistry and Biophysics Polish Academy of Sciences, 5a Pawinskiego St., 02-106, Warsaw, Poland.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University Olomouc, Slechtitelu 27, 771 46, Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65, Brno, Czech Republic. krepl@ibp.cz.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109, Warsaw, Poland. mnowotny@iimcb.gov.pl.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Crossover junction endodeoxyribonuclease RuvC
A, B
169Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: ruvC
EC: 3.1.22.4
Find proteins for Q5SJC4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJC4
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (33-MER)C33synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*CP*TP*GP*CP*CP*GP*AP*TP*TP*C)-3')D,F33synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.409 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.066α = 90.00
b = 108.066β = 90.00
c = 133.281γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development FundCzech RepublicCZ.02.1.01/0.0/0.0/15_003/0000477
Wellcome Trust098022

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release