4YJ0

Crystal structure of the DM domain of human DMRT1 bound to 25mer target DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.814 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An ancient protein-DNA interaction underlying metazoan sex determination.

Murphy, M.W.Lee, J.K.Rojo, S.Gearhart, M.D.Kurahashi, K.Banerjee, S.Loeuille, G.A.Bashamboo, A.McElreavey, K.Zarkower, D.Aihara, H.Bardwell, V.J.

(2015) Nat.Struct.Mol.Biol. 22: 442-451

  • DOI: 10.1038/nsmb.3032

  • PubMed Abstract: 
  • DMRT transcription factors are deeply conserved regulators of metazoan sexual development. They share the DM DNA-binding domain, a unique intertwined double zinc-binding module followed by a C-terminal recognition helix, which binds a pseudopalindrom ...

    DMRT transcription factors are deeply conserved regulators of metazoan sexual development. They share the DM DNA-binding domain, a unique intertwined double zinc-binding module followed by a C-terminal recognition helix, which binds a pseudopalindromic target DNA. Here we show that DMRT proteins use a unique binding interaction, inserting two adjacent antiparallel recognition helices into a widened DNA major groove to make base-specific contacts. Versatility in how specific base contacts are made allows human DMRT1 to use multiple DNA binding modes (tetramer, trimer and dimer). Chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) indicates that multiple DNA binding modes also are used in vivo. We show that mutations affecting residues crucial for DNA recognition are associated with an intersex phenotype in flies and with male-to-female sex reversal in humans. Our results illuminate an ancient molecular interaction underlying much of metazoan sexual development.


    Organizational Affiliation

    Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Doublesex- and mab-3-related transcription factor 1
A, B, C
70Homo sapiensMutation(s): 0 
Gene Names: DMRT1 (DMT1)
Find proteins for Q9Y5R6 (Homo sapiens)
Go to Gene View: DMRT1
Go to UniProtKB:  Q9Y5R6
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (25-MER)D25Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (25-MER)E25Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.814 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 83.185α = 90.00
b = 138.926β = 90.00
c = 141.574γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
RESOLVEphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesGM59152
National Institutes of HealthUnited StatesGM50399
National Institutes of HealthUnited StatesAI087098
National Institutes of HealthUnited StatesGM095558
NIGMSUnited StatesP41 GM103403
COSFranceAction DSDnet BM1303
Institut PasteurFranceProgram Blanc Assistance Publique

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references
  • Version 1.2: 2015-06-10
    Type: Database references