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, 495 (7441), 394-8

Multidomain Integration in the Structure of the HNF-4α Nuclear Receptor Complex


Multidomain Integration in the Structure of the HNF-4α Nuclear Receptor Complex

Vikas Chandra et al. Nature.


The hepatocyte nuclear factor 4α (HNF-4α; also known as NR2A1) is a member of the nuclear receptor (NR) family of transcription factors, which have conserved DNA-binding domains and ligand-binding domains. HNF-4α is the most abundant DNA-binding protein in the liver, where some 40% of the actively transcribed genes have a HNF-4α response element. These regulated genes are largely involved in the hepatic gluconeogenic program and lipid metabolism. In the pancreas HNF-4α is also a master regulator, controlling an estimated 11% of islet genes. HNF-4α protein mutations are linked to maturity-onset diabetes of the young, type 1 (MODY1) and hyperinsulinaemic hypoglycaemia. Previous structural analyses of NRs, although productive in elucidating the structure of individual domains, have lagged behind in revealing the connectivity patterns of NR domains. Here we describe the 2.9 Å crystal structure of the multidomain human HNF-4α homodimer bound to its DNA response element and coactivator-derived peptides. A convergence zone connects multiple receptor domains in an asymmetric fashion, joining distinct elements from each monomer. An arginine target of PRMT1 methylation protrudes directly into this convergence zone and sustains its integrity. A serine target of protein kinase C is also responsible for maintaining domain-domain interactions. These post-translational modifications lead to changes in DNA binding by communicating through the tightly connected surfaces of the quaternary fold. We find that some MODY1 mutations, positioned on the ligand-binding domain and hinge regions of the receptor, compromise DNA binding at a distance by communicating through the interjunctional surfaces of the complex. The overall domain representation of the HNF-4α homodimer is different from that of the PPAR-γ-RXR-α heterodimer, even when both NR complexes are assembled on the same DNA element. Our findings suggest that unique quaternary folds and interdomain connections in NRs could be exploited by small-molecule allosteric modulators that affect distal functions in these polypeptides.

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The authors declare no competing financial interests.


Figure 1
Figure 1. Overall organization of the HNF4α homodimer on DNA
a, Linear depiction of the HNF4α protein domains. b, Electron density map (2fo-fc) for one of the two HNF4α homodimer/DNA complexes of the crystallographic asymmetric unit. c, Superposition of the two independent HNF4α homodimer/DNA complexes in the asymmetric unit. The two homodimeric complexes are colored orange/yellow in one case, and blue/purple in the other. The ligands in the LBD are shown in blue, Zn is shown in grey, and the coactivator peptides are in red/brown. Numbers with prime refer to the upstream positioned subunit. d, The positioning of both LBDs in a complex on top of the upstream DBD fosters high affinity DR1 DNA. e, Contribution of various receptor domains to the DNA binding affinity of HNF4α DNA binding is measured using fluorescent polarization studies with a 5′ FITC-labeled DR1. The x-axis shows concentration of the HNF4α protein, and the y-axis shows the fractional DNA bound. Removal of the AB domain (ΔAB), F-domain (ΔF) or both (ΔABΔF) does not alter the DNA affinity compared to the full-length (FL) receptor. However, removal of the LBD reduces the affinity of the resulting DBD-hinge (DBD) region to a Kd of approximately 6000 nM, whereas the presence of the LBD together with the DBD-hinge (ΔABΔF) allows DNA binding with a Kd of 82 nM (see also Supplementary Table 2).
Figure 2
Figure 2. Domain-domain contacts of HNF4α
a, Circle indicates the convergence center where four domains (both LBDs, the upstream DBD, the downstream hinge) come together. b, Arg-91, located on the surface of the DBD, inserts deeply into a pocket at the base of the LBD-LBD surface. Numbers with prime refer to the upstream positioned subunit. c, Ser-78, positioned on the back-side of the DNA recognition helix, also fosters the convergence of the DBD and the LBDs.
Figure 3
Figure 3. Disease-linked mutations in HNF4α
a, Summary of MODY1 and HH point mutations identified clinically in human populations. b,c, The MODY1 mutations, in many cases (residues in red) map to the “convergence center” of the receptor domains (blue circle in b). d, DNA affinity measurements of the WT and mutant receptors, as described in Figure 1e. See also Supplementary Figure 10 for studies of other disease-linked mutations.
Figure 4
Figure 4. Comparison the HNF4α homodimer and the PPARγ-RXRα heterodimer complexes on DR1 DNA
a, The PPARγ-RXRα heterodimer on DR1, b, The HNF4α homodimer on DR1, and c) their overlap when the DR1 sequences are superimposed, showing the distinct domain-domain arrangements in these two complexes. The two complexes are shown in an identical fashion with respect to the DNA sequence facing the viewer.

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