2MF8

HADDOCK model of MyT1 F4F5 - DNA complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A structural analysis of DNA binding by myelin transcription factor 1 double zinc fingers.

Gamsjaeger, R.O'Connell, M.R.Cubeddu, L.Shepherd, N.E.Lowry, J.A.Kwan, A.H.Vandevenne, M.Swanton, M.K.Matthews, J.M.Mackay, J.P.

(2013) J.Biol.Chem. 288: 35180-35191

  • DOI: 10.1074/jbc.M113.482075

  • PubMed Abstract: 
  • Myelin transcription factor 1 (MyT1/NZF2), a member of the neural zinc-finger (NZF) protein family, is a transcription factor that plays a central role in the developing central nervous system. It has also recently been shown that, in combination wit ...

    Myelin transcription factor 1 (MyT1/NZF2), a member of the neural zinc-finger (NZF) protein family, is a transcription factor that plays a central role in the developing central nervous system. It has also recently been shown that, in combination with two other transcription factors, the highly similar paralog MyT1L is able to direct the differentiation of murine and human stem cells into functional neurons. MyT1 contains seven zinc fingers (ZFs) that are highly conserved throughout the protein and throughout the NZF family. We recently presented a model for the interaction of the fifth ZF of MyT1 with a DNA sequence derived from the promoter of the retinoic acid receptor (RARE) gene. Here, we have used NMR spectroscopy, in combination with surface plasmon resonance and data-driven molecular docking, to delineate the mechanism of DNA binding for double ZF polypeptides derived from MyT1. Our data indicate that a two-ZF unit interacts with the major groove of the entire RARE motif and that both fingers bind in an identical manner and with overall two-fold rotational symmetry, consistent with the palindromic nature of the target DNA. Several key residues located in one of the irregular loops of the ZFs are utilized to achieve specific binding. Analysis of the human and mouse genomes based on our structural data reveals three putative MyT1 target genes involved in neuronal development.


    Organizational Affiliation

    From the School of Molecular Biosciences, University of Sydney, New South Wales 2006, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myelin transcription factor 1
A
93Mus musculusMutation(s): 0 
Gene Names: Myt1 (Kiaa0835, Nzf2)
Find proteins for Q8CFC2 (Mus musculus)
Go to UniProtKB:  Q8CFC2
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*CP*GP*AP*AP*AP*GP*TP*TP*CP*AP*C)-3')B13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*GP*AP*AP*CP*TP*TP*TP*CP*GP*GP*T)-3')C13N/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: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Database references