6O3T

Structural basis of FOXC2 and DNA interactions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

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This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of FOXC2 in Complex with DNA Target.

Li, S.Pradhan, L.Ashur, S.Joshi, A.Nam, H.J.

(2019) ACS Omega 4: 10906-10914

  • DOI: https://doi.org/10.1021/acsomega.9b00756
  • Primary Citation of Related Structures:  
    6O3T

  • PubMed Abstract: 

    Forkhead transcription factor C2 (FOXC2) is a transcription factor regulating vascular and lymphatic development, and its mutations are linked to lymphedema-distichiasis syndrome. FOXC2 is also a crucial regulator of the epithelial-mesenchymal transition processes essential for tumor metastasis. Here, we report the crystal structure of the FOXC2-DNA-binding domain in complex with its cognate DNA. The crystal structure provides the basis of DNA sequence recognition by FOXC2 for the T/CAAAC motif. Helix 3 makes the majority of the DNA-protein interactions and confers the DNA sequence specificity. The computational energy calculation results also validate the structural observations. The FOXC2 and DNA complex structure provides a detailed picture of protein and DNA interactions, which allows us to predict its DNA recognition specificity and impaired functions in mutants identified in human patients.


  • Organizational Affiliation

    Department of Bioengineering, The University of Texas at Dallas, 800 W. Campbell Road, Richardson, Texas 75080, United States.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Forkhead box protein C2A,
D [auth B]
95Homo sapiensMutation(s): 0 
Gene Names: FOXC2FKHL14MFH1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99958 (Homo sapiens)
Explore Q99958 
Go to UniProtKB:  Q99958
PHAROS:  Q99958
GTEx:  ENSG00000176692 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99958
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*GP*CP*CP*CP*G)-3')B [auth C]21synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*CP*GP*GP*GP*CP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*AP*T)-3')C [auth D]21synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.365α = 90
b = 41.812β = 98.3
c = 82.654γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description