2UZK | pdb_00002uzk

Crystal structure of the human FOXO3a-DBD bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.266 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2UZK

This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Human Foxo3A-Dbd/DNA Complex Suggests the Effects of Post-Translational Modification.

Tsai, K.-L.Sun, Y.-J.Huang, C.-Y.Yang, J.-Y.Hung, M.-C.Hsiao, C.-D.

(2007) Nucleic Acids Res 35: 6984

  • DOI: https://doi.org/10.1093/nar/gkm703
  • Primary Citation Related Structures: 
    2UZK

  • PubMed Abstract: 

    FOXO3a is a transcription factor of the FOXO family. The FOXO proteins participate in multiple signaling pathways, and their transcriptional activity is regulated by several post-translational mechanisms, including phosphorylation, acetylation and ubiquitination. Because these post-translational modification sites are located within the C-terminal basic region of the FOXO DNA-binding domain (FOXO-DBD), it is possible that these post-translational modifications could alter the DNA-binding characteristics. To understand how FOXO mediate transcriptional activity, we report here the 2.7 A crystal structure of the DNA-binding domain of FOXO3a (FOXO3a-DBD) bound to a 13-bp DNA duplex containing a FOXO consensus binding sequence (GTAAACA). Based on a unique structural feature in the C-terminal region and results from biochemical and mutational studies, our studies may explain how FOXO-DBD C-terminal phosphorylation by protein kinase B (PKB) or acetylation by cAMP-response element binding protein (CBP) can attenuate the DNA-binding activity and thereby reduce transcriptional activity of FOXO proteins. In addition, we demonstrate that the methyl groups of specific thymine bases within the consensus sequence are important for FOXO3a-DBD recognition of the consensus binding site.


  • Organizational Affiliation
    • Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 37.92 kDa 
  • Atom Count: 2,741 
  • Modeled Residue Count: 241 
  • Deposited Residue Count: 246 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FORKHEAD BOX PROTEIN O3A
A, C
97Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O43524 (Homo sapiens)
Explore O43524 
Go to UniProtKB:  O43524
PHAROS:  O43524
GTEx:  ENSG00000118689 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43524
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*TP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*C)-3'
B, D
13Homo sapiens
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*GP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*AP*G)-3'
E, F
13Homo sapiens
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.266 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.964α = 90
b = 41.964β = 90
c = 354.817γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description