Crystal structure of TALE homeobox domain transcription factor TGIF1 with its consensus DNA

  • Classification: TRANSCRIPTION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • 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

  • Resolution: 2.42 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1093/nar/gky680
  • Primary Citation of Related Structures:  
    6FQP, 6FQQ

  • 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. 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

    Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Homeobox protein TGIF1C [auth A],
D [auth B]
101Homo sapiensMutation(s): 0 
Gene Names: TGIF1TGIF
UniProt & NIH Common Fund Data Resources
Find proteins for Q15583 (Homo sapiens)
Explore Q15583 
Go to UniProtKB:  Q15583
PHAROS:  Q15583
GTEx:  ENSG00000177426 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15583
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
B [auth M]
16Homo sapiens
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.42 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.851α = 90
b = 67.248β = 90
c = 102.315γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2014-53787-P
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: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description