3UKG

Crystal structure of Rap1/DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 3197-3207

  • DOI: 10.1093/nar/gkr1166
  • Also Cited By: 4GFB

  • PubMed Abstract: 
  • Rap1 is an essential DNA-binding factor from the yeast Saccharomyces cerevisiae involved in transcription and telomere maintenance. Its binding to DNA targets Rap1 at particular loci, and may optimize its ability to form functional macromolecular ass ...

    Rap1 is an essential DNA-binding factor from the yeast Saccharomyces cerevisiae involved in transcription and telomere maintenance. Its binding to DNA targets Rap1 at particular loci, and may optimize its ability to form functional macromolecular assemblies. It is a modular protein, rich in large potentially unfolded regions, and comprising BRCT, Myb and RCT well-structured domains. Here, we present the architectures of Rap1 and a Rap1/DNA complex, built through a step-by-step integration of small angle X-ray scattering, X-ray crystallography and nuclear magnetic resonance data. Our results reveal Rap1 structural adjustment upon DNA binding that involves a specific orientation of the C-terminal (RCT) domain with regard to the DNA binding domain (DBD). Crystal structure of DBD in complex with a long DNA identifies an essential wrapping loop, which constrains the orientation of the RCT and affects Rap1 affinity to DNA. Based on our structural information, we propose a model for Rap1 assembly at telomere.


    Organizational Affiliation

    Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-binding protein RAP1
A
242Saccharomyces 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 DNAC31N/A
Entity ID: 3
MoleculeChainsLengthOrganism
telomeric DNAD31N/A
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: 2.95 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.595α = 90.00
b = 102.944β = 90.00
c = 116.755γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
MOSFLMdata reduction
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-01-11
    Type: Database references
  • Version 1.2: 2012-05-09
    Type: Database references