5X07

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.796 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • 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 du ...

    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

    Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hepatocyte nuclear factor 3-beta
F, C, I, L
104Homo sapiensGene Names: FOXA2 (HNF3B, TCF3B)
Find proteins for Q9Y261 (Homo sapiens)
Go to Gene View: FOXA2
Go to UniProtKB:  Q9Y261
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')D,A,G,J16Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')E,B,H,K16Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.796 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 195.126α = 90.00
b = 71.932β = 103.14
c = 72.155γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
PHENIXrefinement
HKL-3000data processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

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