3CBB

Crystal Structure of Hepatocyte Nuclear Factor 4alpha in complex with DNA: Diabetes Gene Product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of natural promoter recognition by a unique nuclear receptor, HNF4alpha. Diabetes gene product.

Lu, P.Rha, G.B.Melikishvili, M.Wu, G.Adkins, B.C.Fried, M.G.Chi, Y.I.

(2008) J Biol Chem 283: 33685-33697

  • DOI: 10.1074/jbc.M806213200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • HNF4alpha (hepatocyte nuclear factor 4alpha) plays an essential role in the development and function of vertebrate organs, including hepatocytes and pancreatic beta-cells by regulating expression of multiple genes involved in organ development, nutrient transport, and diverse metabolic pathways ...

    HNF4alpha (hepatocyte nuclear factor 4alpha) plays an essential role in the development and function of vertebrate organs, including hepatocytes and pancreatic beta-cells by regulating expression of multiple genes involved in organ development, nutrient transport, and diverse metabolic pathways. As such, HNF4alpha is a culprit gene product for a monogenic and dominantly inherited form of diabetes, known as maturity onset diabetes of the young (MODY). As a unique member of the nuclear receptor superfamily, HNF4alpha recognizes target genes containing two hexanucleotide direct repeat DNA-response elements separated by one base pair (DR1) by exclusively forming a cooperative homodimer. We describe here the 2.0 angstroms crystal structure of human HNF4alpha DNA binding domain in complex with a high affinity promoter element of another MODY gene, HNF1alpha, which reveals the molecular basis of unique target gene selection/recognition, DNA binding cooperativity, and dysfunction caused by diabetes-causing mutations. The predicted effects of MODY mutations have been tested by a set of biochemical and functional studies, which show that, in contrast to other MODY gene products, the subtle disruption of HNF4alpha molecular function can cause significant effects in afflicted MODY patients.


    Related Citations: 
    • Crystallization of Hepatocyte Nuclear Factor 4alpha (HNF4alpha) in complex with the HNF1alpha Promoter Element
      Lu, P., Liu, J., Melikishvili, M., Fried, M.G., Chi, Y.-I.
      () To be published --: --

    Organizational Affiliation

    Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hepatocyte Nuclear Factor 4-alpha, DNA binding domainA, B78Homo sapiensMutation(s): 0 
Gene Names: HNF4AHNF4NR2A1TCF14
Find proteins for P41235 (Homo sapiens)
Explore P41235 
Go to UniProtKB:  P41235
NIH Common Fund Data Resources
PHAROS  P41235
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
Hepatocyte Nuclear Factor 4-alpha promoter element DNAC21N/A

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
Hepatocyte Nuclear Factor 4-alpha promoter element DNAD21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.628α = 90
b = 35.425β = 119.36
c = 70.985γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description