1M6U

Crystal Structure of a Novel DNA-binding domain from Ndt80, a Transcriptional Activator Required for Meiosis in Yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast

Montano, S.P.Cote, M.L.Fingerman, I.Pierce, M.Vershon, A.K.Georgiadis, M.M.

(2002) Proc.Natl.Acad.Sci.USA 99: 14041-14046

  • DOI: 10.1073/pnas.222312199
  • Primary Citation of Related Structures:  1M7U

  • PubMed Abstract: 
  • Ndt80 is a transcriptional activator required for meiosis in the yeast Saccharomyces cerevisiae. Here, we report the crystal structure at 2.3 A resolution of the DNA-binding domain of Ndt80 experimentally phased by using the anomalous and isomorphous ...

    Ndt80 is a transcriptional activator required for meiosis in the yeast Saccharomyces cerevisiae. Here, we report the crystal structure at 2.3 A resolution of the DNA-binding domain of Ndt80 experimentally phased by using the anomalous and isomorphous signal from a single ordered Se atom per molecule of 272-aa residues. The structure reveals a single approximately 32-kDa domain with a distinct fold comprising a beta-sandwich core elaborated with seven additional beta-sheets and three short alpha-helices. Inspired by the structure, we have performed a mutational analysis and defined a DNA-binding motif in this domain. The DNA-binding domain of Ndt80 is homologous to a number of proteins from higher eukaryotes, and the residues that we have shown are required for DNA binding by Ndt80 are highly conserved among this group of proteins. These results suggest that Ndt80 is the defining member of a previously uncharacterized family of transcription factors, including the human protein (C11orf9), which has been shown to be highly expressed in invasive or metastatic tumor cells.


    Organizational Affiliation

    Waksman Institute and Department of Chemistry and Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ndt80 protein
A, B
272Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: NDT80 (DAS1)
Find proteins for P38830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38830
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.275α = 90.00
b = 64.897β = 107.52
c = 92.419γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance