6FQQ

Crystal structure of TALE homeobox domain transcription factor TGIF1 double alanine mutant bound to its consensus DNA

  • Classification: TRANSCRIPTION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2018-02-14 Released: 2018-07-25 
  • Deposition Author(s): Guca, E., Macias, M.J.
  • Funding Organization(s): Spanish Ministry of Economy and Competitiveness, COFUND Marie Sklodowska Curie

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

TGIF1 homeodomain interacts with Smad MH1 domain and represses TGF-beta signaling.

Guca, E.Sunol, D.Ruiz, L.Konkol, A.Cordero, J.Torner, C.Aragon, E.Martin-Malpartida, P.Riera, A.Macias, M.J.

(2018) Nucleic Acids Res 46: 9220-9235

  • DOI: 10.1093/nar/gky680
  • Primary Citation of Related Structures:  
    6FQQ, 6FQP

  • PubMed Abstract: 
  • TGIF1 is a multifunctional protein that represses TGF-β-activated transcription by interacting with Smad2-Smad4 complexes. We found that the complex structure of TGIF1-HD bound to the TGACA motif revealed a combined binding mode that involves the HD core and the major groove, on the one hand, and the amino-terminal (N-term) arm and the minor groove of the DNA, on the other ...

    TGIF1 is a multifunctional protein that represses TGF-β-activated transcription by interacting with Smad2-Smad4 complexes. We found that the complex structure of TGIF1-HD bound to the TGACA motif revealed a combined binding mode that involves the HD core and the major groove, on the one hand, and the amino-terminal (N-term) arm and the minor groove of the DNA, on the other. We also show that TGIF1-HD interacts with the MH1 domain of Smad proteins, thereby indicating that TGIF1-HD is also a protein-binding domain. Moreover, the formation of the HD-MH1 complex partially hinders the DNA-binding site of the complex, preventing the efficient interaction of TGIF1-HD with DNA. We propose that the binding of the TGIF1 C-term to the Smad2-MH2 domain brings both the HD and MH1 domain into close proximity. This local proximity facilitates the interaction of these DNA-binding domains, thus strengthening the formation of the protein complex versus DNA binding. Once the protein complex has been formed, the TGIF1-Smad system would be released from promoters/enhancers, thereby illustrating one of the mechanisms used by TGIF1 to exert its function as an active repressor of Smad-induced TGF-β signaling.


    Organizational Affiliation

    ICREA, Passeig Lluís Companys 23, 08010-Barcelona, Spain.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein TGIF1A, D [auth B], G [auth D], H [auth E]71Homo sapiensMutation(s): 2 
Gene Names: TGIF1TGIF
UniProt & NIH Common Fund Data Resources
Find proteins for Q15583 (Homo sapiens)
Explore Q15583 
Go to UniProtKB:  Q15583
PHAROS:  Q15583
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*T)-3')E [auth G], F [auth H], B [auth L], C [auth M]16Homo sapiens
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CL
    Query on CL

    Download Ideal Coordinates CCD File 
    I [auth A]CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.25 Å
    • R-Value Free: 0.273 
    • R-Value Work: 0.215 
    • R-Value Observed: 0.218 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 60.058α = 90
    b = 93.016β = 90
    c = 100.711γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    XDSdata reduction
    SCALAdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2018-02-14 
    • Released Date: 2018-07-25 
    • Deposition Author(s): Guca, E., Macias, M.J.

    Funding OrganizationLocationGrant Number
    Spanish Ministry of Economy and CompetitivenessSpainBFU2014-53787P
    COFUND Marie Sklodowska CurieSpainIRBPostPro2.0 600404

    Revision History  (Full details and data files)

    • Version 1.0: 2018-07-25
      Type: Initial release
    • Version 1.1: 2018-08-29
      Changes: Data collection, Database references
    • Version 1.2: 2018-10-10
      Changes: Data collection, Database references
    • Version 1.3: 2019-11-06
      Changes: Data collection, Refinement description