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 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 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.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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
GTEx:  ENSG00000177426 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15583
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*T)-3')B [auth L],
C [auth M],
E [auth G],
F [auth H]
16Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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


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
  • Version 1.4: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description