2VI6

Crystal Structure of the Nanog Homeodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog.

Jauch, R.Ng, C.K.L.Saitakendu, K.S.Stevens, R.C.Kolatkar, P.R.

(2008) J.Mol.Biol. 376: 758

  • DOI: 10.1016/j.jmb.2007.11.091

  • PubMed Abstract: 
  • The transcription factor Nanog is an upstream regulator in early mammalian development and a key determinant of pluripotency in embryonic stem cells. Nanog binds to promoter elements of hundreds of target genes and regulates their expression by an as ...

    The transcription factor Nanog is an upstream regulator in early mammalian development and a key determinant of pluripotency in embryonic stem cells. Nanog binds to promoter elements of hundreds of target genes and regulates their expression by an as yet unknown mechanism. Here, we report the crystal structure of the murine Nanog homeodomain (HD) and analysis of its interaction with a DNA element derived from the Tcf3 promoter. Two Nanog amino acid pairs, unique among HD sequences, appear to affect the mechanism of nonspecific DNA recognition as well as maintain the integrity of the structural scaffold. To assess selective DNA recognition by Nanog, we performed electrophoretic mobility shift assays using a panel of modified DNA binding sites and found that Nanog HD preferentially binds the TAAT(G/T)(G/T) motif. A series of rational mutagenesis experiments probing the role of six variant residues of Nanog on its DNA binding function establish their role in affecting binding affinity but not binding specificity. Together, the structural and functional evidence establish Nanog as a distant member of a Q50-type HD despite having considerable variation at the sequence level.


    Organizational Affiliation

    Laboratory of Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore. jauchr@gis.a-star.edu.sg




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HOMEOBOX PROTEIN NANOG
A, B, C, D, E, F, G, H
62Mus musculusMutation(s): 0 
Gene Names: Nanog (Ecat4, Enk)
Find proteins for Q80Z64 (Mus musculus)
Go to UniProtKB:  Q80Z64
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.318α = 90.00
b = 114.771β = 98.68
c = 62.771γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance