6XAT

Crystal structure of the human FoxP4 DNA binding Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Unraveling the folding and dimerization properties of the human FoxP subfamily of transcription factors.

Villalobos, P.Carvajal, A.I.Castro-Fernandez, V.Babul, J.Ramirez-Sarmiento, C.A.Medina, E.

(2023) FEBS Lett 597: 1894-1905

  • DOI: https://doi.org/10.1002/1873-3468.14665
  • Primary Citation of Related Structures:  
    6XAT

  • PubMed Abstract: 

    Human FoxP proteins share a highly conserved DNA-binding domain that dimerizes via three-dimensional domain swapping, although showing varying oligomerization propensities among its members. Here, we present an experimental and computational characterization of all human FoxP proteins to unravel how their amino acid substitutions impact their folding and dimerization mechanism. We solved the crystal structure of the forkhead domain of FoxP4 to then perform a comparison across all members, finding that their sequence changes impact not only the structural heterogeneity of their forkhead domains but also the protein-protein association energy barrier. Lastly, we demonstrate that the accumulation of a monomeric intermediate is an oligomerization-dependent feature rather than a common aspect of monomers and dimers in this protein subfamily.


  • Organizational Affiliation

    Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FOXP4 protein110Homo sapiensMutation(s): 0 
Gene Names: FOXP4
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVH2 (Homo sapiens)
Explore Q8IVH2 
Go to UniProtKB:  Q8IVH2
PHAROS:  Q8IVH2
GTEx:  ENSG00000137166 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IVH2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.449α = 90
b = 70.648β = 90
c = 63.469γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChileFONDECYT 1170701
Other governmentChileFONDECYT 21151101
Other governmentChileFONDEQUIP EQM 120208
Other governmentChileCONICYT, Proyectos REDES ETAPA INICIAL, Convocatoria 2017 REDI170497
Other governmentBrazilBrazilian Synchrotron Light Laboratory, Proposals 20170411
Other governmentChileCONICYT, FONDECYT 11140601

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-01-31
    Changes: Database references