1ODH

Structure of the GCM domain bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Gcm Domain-DNA Complex: A DNA-Binding Domain with a Novel Fold and Mode of Target Site Recognition

Cohen, S.X.Moulin, M.Hashemolhosseini, S.Kilian, K.Wegner, M.Muller, C.W.

(2003) Embo J. 22: 1835

  • DOI: 10.1093/emboj/cdg182

  • PubMed Abstract: 
  • Glia cell missing (GCM) transcription factors form a small family of transcriptional regulators in metazoans. The prototypical Drosophila GCM protein directs the differentiation of neuron precursor cells into glia cells, whereas mammalian GCM protein ...

    Glia cell missing (GCM) transcription factors form a small family of transcriptional regulators in metazoans. The prototypical Drosophila GCM protein directs the differentiation of neuron precursor cells into glia cells, whereas mammalian GCM proteins are involved in placenta and parathyroid development. GCM proteins share a highly conserved 150 amino acid residue region responsible for DNA binding, known as the GCM domain. Here we present the crystal structure of the GCM domain from murine GCMa bound to its octameric DNA target site at 2.85 A resolution. The GCM domain exhibits a novel fold consisting of two domains tethered together by one of two structural Zn ions. We observe the novel use of a beta-sheet in DNA recognition, whereby a five- stranded beta-sheet protrudes into the major groove perpendicular to the DNA axis. The structure combined with mutational analysis of the target site and of DNA-contacting residues provides insight into DNA recognition by this new type of Zn-containing DNA-binding domain.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble Cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MGCM1
A
174Mus musculusMutation(s): 0 
Gene Names: Gcm1 (Gcma)
Find proteins for P70348 (Mus musculus)
Go to UniProtKB:  P70348
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*TP*GP*CP*GP*GP*GP*TP *GP*CP*A)-3'C13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*GP*CP*AP*CP*CP*CP*GP*CP*AP *TP*CP*G)-3'D13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.810α = 90.00
b = 52.910β = 103.24
c = 62.970γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKLdata reduction
CNSrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance