5X07

Crystal structure of FOXA2 DNA binding domain bound to a full consensus DNA site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

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Literature

Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site

Li, J., Machado, A.C.D., Guo, M., Sagendorf, J.M., Zhou, Z., Jiang, L., Chen, X., Wu, D., Qu, L., Chen, Z., Chen, L., Rohs, R., Chen, Y.

(2017) Biochemistry 56: 3745-3753

  • DOI: 10.1021/acs.biochem.7b00211
  • Primary Citation of Related Structures:  
    5X07

  • PubMed Abstract: 

    • FOXA2, a member of the forkhead family of transcription factors, plays essential roles in liver development and bile acid homeostasis. In this study, we report a 2.8 Å co-crystal structure of the FOXA2 DNA-binding domain (FOXA2-DBD) bound to a DNA duplex containing a forkhead consensus binding site (GTAAACA) ...

    FOXA2, a member of the forkhead family of transcription factors, plays essential roles in liver development and bile acid homeostasis. In this study, we report a 2.8 Å co-crystal structure of the FOXA2 DNA-binding domain (FOXA2-DBD) bound to a DNA duplex containing a forkhead consensus binding site (GTAAACA). The FOXA2-DBD adopts the canonical winged-helix fold, with helix H3 and wing 1 regions mainly mediating the DNA recognition. Although the wing 2 region was not defined in the structure, isothermal titration calorimetry assays suggested that this region was required for optimal DNA binding. Structure comparison with the FOXA3-DBD bound to DNA revealed more major groove contacts and fewer minor groove contacts in the FOXA2 structure than in the FOXA3 structure. Structure comparison with the FOXO1-DBD bound to DNA showed that different forkhead proteins could induce different DNA conformations upon binding to identical DNA sequences. Our findings provide the structural basis for FOXA2 protein binding to a consensus forkhead site and elucidate how members of the forkhead protein family bind different DNA sites.

    Organizational Affiliation: 

    Collaborative Innovation Center for Cancer Medicine , Guangzhou, Guangdong 510060, China.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte nuclear factor 3-betaF [auth C],
C [auth F],
I,
L		104Homo sapiensMutation(s): 0 
Gene Names: FOXA2, HNF3B, TCF3B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y261 (Homo sapiens)
Explore Q9Y261 
Go to UniProtKB:  Q9Y261
PHAROS:  Q9Y261
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y261
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')D [auth A],
A [auth D],
G,
J		16Homo sapiens
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')E [auth B],
B [auth E],
H,
K		16Homo sapiens
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 195.126α = 90
b = 71.932β = 103.14
c = 72.155γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data processing
HKL-3000data collection

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81372904
National Natural Science Foundation of ChinaChina81570537
National Natural Science Foundation of ChinaChina81272971

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Advisory, Derived calculations