3CBB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 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

  • 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, nutri ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hepatocyte Nuclear Factor 4-alpha, DNA binding domain
A, B
78Homo sapiensMutation(s): 0 
Gene Names: HNF4A (HNF4, NR2A1, TCF14)
Find proteins for P41235 (Homo sapiens)
Go to Gene View: HNF4A
Go to UniProtKB:  P41235
Entity ID: 1
MoleculeChainsLengthOrganism
Hepatocyte Nuclear Factor 4-alpha promoter element DNAC21N/A
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 SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 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 = 90.00
b = 35.425β = 119.36
c = 70.985γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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