4GFB

Rap1/DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity.

Le Bihan, Y.V.Matot, B.Pietrement, O.Giraud-Panis, M.J.Gasparini, S.Le Cam, E.Gilson, E.Sclavi, B.Miron, S.Le Du, M.H.

(2013) Acta Crystallogr.,Sect.D 69: 409-419

  • DOI: 10.1107/S0907444912049311

  • PubMed Abstract: 
  • Repressor activator protein 1 (Rap1) is an essential factor involved in transcription and telomere stability in the budding yeast Saccharomyces cerevisiae. Its interaction with DNA causes hypersensitivity to potassium permanganate, suggesting local D ...

    Repressor activator protein 1 (Rap1) is an essential factor involved in transcription and telomere stability in the budding yeast Saccharomyces cerevisiae. Its interaction with DNA causes hypersensitivity to potassium permanganate, suggesting local DNA melting and/or distortion. In this study, various Rap1-DNA crystal forms were obtained using specifically designed crystal screens. Analysis of the DNA conformation showed that its distortion was not sufficient to explain the permanganate reactivity. However, anomalous data collected at the Mn edge using a Rap1-DNA crystal soaked in potassium permanganate solution indicated that the DNA conformation in the crystal was compatible with interaction with permanganate ions. Sequence-conservation analysis revealed that double-Myb-containing Rap1 proteins all carry a fully conserved Arg580 at a position that may favour interaction with permanganate ions, although it is not involved in the hypersensitive cytosine distortion. Permanganate reactivity assays with wild-type Rap1 and the Rap1[R580A] mutant demonstrated that Arg580 is essential for hypersensitivity. AFM experiments showed that wild-type Rap1 and the Rap1[R580A] mutant interact with DNA over 16 successive binding sites, leading to local DNA stiffening but not to accumulation of the observed local distortion. Therefore, Rap1 may cause permanganate hypersensitivity of DNA by forming a pocket between the reactive cytosine and Arg580, driving the permanganate ion towards the C5-C6 bond of the cytosine.


    Related Citations: 
    • The orientation of the C-terminal domain of the Saccharomyces cerevisiae Rap1 protein is determined by its binding to DNA.
      Matot, B.,Le Bihan, Y.-V.,Lescasse, R.,Perez, J.,Miron, S.,David, G.,Castaing, B.,Weber, P.,Raynal, B.,Zinn-Justin, S.,Gasparini, S.,Le Du, M.-H.
      (2012) Nucleic Acids Res. 40: 3197


    Organizational Affiliation

    CEA/DSV/IBiTec-S/SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, CNRS UMR 8221, University Paris-Sud, B√Ętiment 144, CE Saclay, 91191 Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-binding protein RAP1
A
272Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RAP1 (GRF1, TUF1)
Find proteins for P11938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P11938
Entity ID: 2
MoleculeChainsLengthOrganism
telomeric DNAC31Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
telomeric DNAD31Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.830α = 90.00
b = 122.650β = 90.00
c = 149.450γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XDSdata scaling
ADSCdata collection
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release