7TDW | pdb_00007tdw

Structure of FOXP3-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 
    0.359 (Depositor), 0.358 (DCC) 
  • R-Value Work: 
    0.335 (Depositor), 0.339 (DCC) 
  • R-Value Observed: 
    0.336 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7TDW

This is version 2.0 of the entry. See complete history

Literature

The transcription factor FoxP3 can fold into two dimerization states with divergent implications for regulatory T cell function and immune homeostasis.

Leng, F.Zhang, W.Ramirez, R.N.Leon, J.Zhong, Y.Hou, L.Yuki, K.van der Veeken, J.Rudensky, A.Y.Benoist, C.Hur, S.

(2022) Immunity 55: 1354

  • DOI: https://doi.org/10.1016/j.immuni.2022.07.002
  • Primary Citation Related Structures: 
    7TDW, 7TDX

  • PubMed Abstract: 

    FoxP3 is an essential transcription factor (TF) for immunologic homeostasis, but how it utilizes the common forkhead DNA-binding domain (DBD) to perform its unique function remains poorly understood. We here demonstrated that unlike other known forkhead TFs, FoxP3 formed a head-to-head dimer using a unique linker (Runx1-binding region [RBR]) preceding the forkhead domain. Head-to-head dimerization conferred distinct DNA-binding specificity and created a docking site for the cofactor Runx1. RBR was also important for proper folding of the forkhead domain, as truncation of RBR induced domain-swap dimerization of forkhead, which was previously considered the physiological form of FoxP3. Rather, swap-dimerization impaired FoxP3 function, as demonstrated with the disease-causing mutation R337Q, whereas a swap-suppressive mutation largely rescued R337Q-mediated functional impairment. Altogether, our findings suggest that FoxP3 can fold into two distinct dimerization states: head-to-head dimerization representing functional specialization of an ancient DBD and swap dimerization associated with impaired functions.


  • Organizational Affiliation
    • Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 28.76 kDa 
  • Atom Count: 1,349 
  • Modeled Residue Count: 118 
  • Deposited Residue Count: 197 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Forkhead box P3169Mus musculusMutation(s): 0 
Gene Names: Foxp3
UniProt
Find proteins for Q99JB6 (Mus musculus)
Explore Q99JB6 
Go to UniProtKB:  Q99JB6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99JB6
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*AP*CP*TP*C)-3')14Mus musculus
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*AP*GP*TP*AP*AP*AP*CP*AP*AP*AP*TP*TP*T)-3')14Mus musculus
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free:  0.359 (Depositor), 0.358 (DCC) 
  • R-Value Work:  0.335 (Depositor), 0.339 (DCC) 
  • R-Value Observed: 0.336 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.092α = 90
b = 92.092β = 90
c = 179.398γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2022-08-24
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 2.0: 2025-12-10
    Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary