4YJ0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.81 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1038/nsmb.3032
  • Primary Citation of Related Structures:  
    4YJ0

  • 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 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

    1] Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA. [2] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Doublesex- and mab-3-related transcription factor 1
A, B, C
70Homo sapiensMutation(s): 0 
Gene Names: DMRT1DMT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5R6 (Homo sapiens)
Explore Q9Y5R6 
Go to UniProtKB:  Q9Y5R6
PHAROS:  Q9Y5R6
GTEx:  ENSG00000137090 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5R6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (25-MER)25Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (25-MER)25Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.81 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.185α = 90
b = 138.926β = 90
c = 141.574γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
RESOLVEphasing
XDSdata reduction

Structure Validation

View Full Validation Report



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
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesP41 GM103403
COSFranceAction DSDnet BM1303
Institut PasteurFranceProgram Blanc Assistance Publique

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2015-06-03
    Changes: Database references
  • Version 1.2: 2015-06-10
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2022-03-30
    Changes: Author supporting evidence, Database references