4WK8

FOXP3 forms a domain-swapped dimer to bridge DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4006 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.

Chen, Y.Chen, C.Zhang, Z.Liu, C.C.Johnson, M.E.Espinoza, C.A.Edsall, L.E.Ren, B.Zhou, X.J.Grant, S.F.Wells, A.D.Chen, L.

(2015) Nucleic Acids Res. 43: 1268-1282

  • DOI: 10.1093/nar/gku1373

  • PubMed Abstract: 
  • FOXP3 is a lineage-specific transcription factor that is required for regulatory T cell development and function. In this study, we determined the crystal structure of the FOXP3 forkhead domain bound to DNA. The structure reveals that FOXP3 can form ...

    FOXP3 is a lineage-specific transcription factor that is required for regulatory T cell development and function. In this study, we determined the crystal structure of the FOXP3 forkhead domain bound to DNA. The structure reveals that FOXP3 can form a stable domain-swapped dimer to bridge DNA in the absence of cofactors, suggesting that FOXP3 may play a role in long-range gene interactions. To test this hypothesis, we used circular chromosome conformation capture coupled with high throughput sequencing (4C-seq) to analyze FOXP3-dependent genomic contacts around a known FOXP3-bound locus, Ptpn22. Our studies reveal that FOXP3 induces significant changes in the chromatin contacts between the Ptpn22 locus and other Foxp3-regulated genes, reflecting a mechanism by which FOXP3 reorganizes the genome architecture to coordinate the expression of its target genes. Our results suggest that FOXP3 mediates long-range chromatin interactions as part of its mechanisms to regulate specific gene expression in regulatory T cells.


    Organizational Affiliation

    Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Forkhead box protein P3
F, G
82Homo sapiensMutation(s): 0 
Gene Names: FOXP3 (IPEX)
Find proteins for Q9BZS1 (Homo sapiens)
Go to Gene View: FOXP3
Go to UniProtKB:  Q9BZS1
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*G)-3')A21synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*T)-3')B21synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4006 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.431α = 90.00
b = 84.837β = 90.00
c = 68.310γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-10-01 
  • Released Date: 2015-01-21 
  • Deposition Author(s): Chen, Y., Chen, L.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM064642
National Natural Science Foundation of ChinaChina81372904
National Natural Science Foundation of ChinaChina81272971

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary