8PI9

DNA binding domain of HNF-1A bound to P2-HNF4A promoter DNA variant (P2 -181G>A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular mechanism of HNF-1A-mediated HNF4A gene regulation and promoter-driven HNF4A-MODY diabetes.

Kind, L.Molnes, J.Tjora, E.Raasakka, A.Myllykoski, M.Colclough, K.Saint-Martin, C.Adelfalk, C.Dusatkova, P.Pruhova, S.Valtonen-Andre, C.Bellanne-Chantelot, C.Arnesen, T.Kursula, P.Njolstad, P.R.

(2024) JCI Insight 9

  • DOI: https://doi.org/10.1172/jci.insight.175278
  • Primary Citation of Related Structures:  
    8PI7, 8PI8, 8PI9, 8PIA

  • PubMed Abstract: 

    Monogenic diabetes is a gateway to precision medicine through molecular mechanistic insight. Hepatocyte nuclear factor 1A (HNF-1A) and HNF-4A are transcription factors that engage in crossregulatory gene transcription networks to maintain glucose-stimulated insulin secretion in pancreatic β cells. Variants in the HNF1A and HNF4A genes are associated with maturity-onset diabetes of the young (MODY). Here, we explored 4 variants in the P2-HNF4A promoter region: 3 in the HNF-1A binding site and 1 close to the site, which were identified in 63 individuals from 21 families of different MODY disease registries across Europe. Our goal was to study the disease causality for these variants and to investigate diabetes mechanisms on the molecular level. We solved a crystal structure of HNF-1A bound to the P2-HNF4A promoter and established a set of techniques to probe HNF-1A binding and transcriptional activity toward different promoter variants. We used isothermal titration calorimetry, biolayer interferometry, x-ray crystallography, and transactivation assays, which revealed changes in HNF-1A binding or transcriptional activities for all 4 P2-HNF4A variants. Our results suggest distinct disease mechanisms of the promoter variants, which can be correlated with clinical phenotype, such as age of diagnosis of diabetes, and be important tools for clinical utility in precision medicine.


  • Organizational Affiliation

    Department of Biomedicine and.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte nuclear factor 1-alphaC [auth A],
D [auth B]
198Homo sapiensMutation(s): 0 
Gene Names: HNF1ATCF1
UniProt & NIH Common Fund Data Resources
Find proteins for P20823 (Homo sapiens)
Explore P20823 
Go to UniProtKB:  P20823
GTEx:  ENSG00000135100 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20823
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
Chains: EA [auth E]21Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
Chains: FB [auth F]21Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.008α = 90
b = 53.065β = 90
c = 202.671γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway245828
Research Council of NorwayNorway245922
Research Council of NorwayNorway240413
Novo Nordisk FoundationDenmark54741

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release