3G73

Structure of the FOXM1 DNA binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence

Littler, D.R.Alvarez-Fernandez, M.Stein, A.Hibbert, R.G.Heidebrecht, T.Aloy, P.Medema, R.H.Perrakis, A.

(2010) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkq194
  • Primary Citation of Related Structures:  
    3G73

  • PubMed Abstract: 
  • FoxM1 is a member of the Forkhead family of transcription factors and is implicated in inducing cell proliferation and some forms of tumorigenesis. It binds promoter regions with a preference for tandem repeats of a consensus 'TAAACA' recognition sequence ...

    FoxM1 is a member of the Forkhead family of transcription factors and is implicated in inducing cell proliferation and some forms of tumorigenesis. It binds promoter regions with a preference for tandem repeats of a consensus 'TAAACA' recognition sequence. The affinity of the isolated FoxM1 DNA-binding domain for this site is in the micromolar range, lower than observed for other Forkhead proteins. To explain these FoxM1 features, we determined the crystal structure of its DNA-binding domain in complex with a tandem recognition sequence. FoxM1 adopts the winged-helix fold, typical of the Forkhead family. Neither 'wing' of the fold however, makes significant contacts with the DNA, while the second, C-terminal, wing adopts an unusual ordered conformation across the back of the molecule. The lack of standard DNA-'wing' interactions may be a reason for FoxM1's relatively low affinity. The role of the 'wings' is possibly undertaken by other FoxM1 regions outside the DBD, that could interact with the target DNA directly or mediate interactions with other binding partners. Finally, we were unable to show a clear preference for tandem consensus site recognition in DNA-binding, transcription activation or bioinformatics analysis; FoxM1's moniker, 'Trident', is not supported by our data.


    Organizational Affiliation

    Department of Biochemistry, The Netherlands Cancer Institute, Plesmaanlaan 121, 1066 CX, Amsterdam, The Netherlands.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Forkhead box protein M1A, B142Homo sapiensMutation(s): 0 
Gene Names: FKHL16FOXM1HFH11MPP2WIN
UniProt & NIH Common Fund Data Resources
Find proteins for Q08050 (Homo sapiens)
Explore Q08050 
Go to UniProtKB:  Q08050
PHAROS:  Q08050
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*AP*AP*TP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*GP*CP*CP*CP*G)-3')C21N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*TP*CP*GP*GP*GP*CP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*AP*T)-3')D21N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], F [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.07α = 90
b = 119.75β = 90
c = 152.97γ = 90
Software Package:
Software NamePurpose
DNAdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance