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. 2011 May;18(5):556-63.
doi: 10.1038/nsmb.2046. Epub 2011 Apr 10.

DNA binding alters coactivator interaction surfaces of the intact VDR-RXR complex

Jun Zhang  1 , Michael J Chalmers, Keith R Stayrook, Lorri L Burris, Yongjun Wang, Scott A Busby, Bruce D Pascal, Ruben D Garcia-Ordonez, John B Bruning, Monica A Istrate, Douglas J Kojetin, Jeffrey A Dodge, Thomas P Burris, Patrick R Griffin
Affiliations

DNA binding alters coactivator interaction surfaces of the intact VDR-RXR complex

Jun Zhang et al. Nat Struct Mol Biol. 2011 May.

Abstract

The vitamin D receptor (VDR) functions as an obligate heterodimer in complex with the retinoid X receptor (RXR). These nuclear receptors are multidomain proteins, and it is unclear how various domains interact with one another within the nuclear receptor heterodimer. Here, we show that binding of intact heterodimer to DNA alters the receptor dynamics in regions remote from the DNA-binding domains (DBDs), including the coactivator binding surfaces of both co-receptors, and that the sequence of the DNA response element can determine these dynamics. Furthermore, agonist binding to the heterodimer results in changes in the stability of the VDR DBD, indicating that the ligand itself may play a role in DNA recognition. These data suggest a mechanism by which nuclear receptors show promoter specificity and have differential effects on various target genes, providing insight into the function of selective nuclear receptor modulators.

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Figures

Figure 1
Figure 1. The interactions along the dimer interface of the RXR-VDR heterodimer
(a) The addition of RXR induced conformational changes in VDR LBD. The average differential HDX of VDR LBD vs. VDR LBD:RXR (Supplementary Table 1b(i–1)) mapped onto VDR LBD-RXR complex docking model. (b) The addition of VDR induced conformational changes in RXR. The average differential HDX of RXR vs. RXR:VDR (Supplementary Table 1c(i–2)) mapped onto RXR-VDR heterodimer docking model. Note: The uniform color legends indicating the differential HDX between two states were used throughout the entire manuscript and they were shown in Supplementary Table 1. The regions in the structural model colored in white mean they are not covered in this study.
Figure 1
Figure 1. The interactions along the dimer interface of the RXR-VDR heterodimer
(a) The addition of RXR induced conformational changes in VDR LBD. The average differential HDX of VDR LBD vs. VDR LBD:RXR (Supplementary Table 1b(i–1)) mapped onto VDR LBD-RXR complex docking model. (b) The addition of VDR induced conformational changes in RXR. The average differential HDX of RXR vs. RXR:VDR (Supplementary Table 1c(i–2)) mapped onto RXR-VDR heterodimer docking model. Note: The uniform color legends indicating the differential HDX between two states were used throughout the entire manuscript and they were shown in Supplementary Table 1. The regions in the structural model colored in white mean they are not covered in this study.
Figure 2
Figure 2. Ligand-induced domain-domain interactions within the RXR-VDR heterodimer complex
Differential HDX data mapped onto RXR-VDR docking model demonstrates (a) 1,25D3 (Supplementary Tables 1b(ii),and 1c(ii)) (b) 9-cis-RA (Supplementary Tables 1b(iii) and 1c(iii)) induced conformational changes of the RXR-VDR heterodimer complex as shown by comparing the deuterium incorporation of both receptors in the absence presence of ligands. (c) 1,25D3 induced conformational changes of the RXR-VDR heterodimer complex bound by 9-cis-RA (Supplementary Tables 1b(iv) and 1c(iv)). (d) 9-cis-RA induced conformational changes of the RXR-VDR heterodimer complex when bound to 1,25D3 (Supplementary Tables 1b(v) and 1c(v)).
Figure 2
Figure 2. Ligand-induced domain-domain interactions within the RXR-VDR heterodimer complex
Differential HDX data mapped onto RXR-VDR docking model demonstrates (a) 1,25D3 (Supplementary Tables 1b(ii),and 1c(ii)) (b) 9-cis-RA (Supplementary Tables 1b(iii) and 1c(iii)) induced conformational changes of the RXR-VDR heterodimer complex as shown by comparing the deuterium incorporation of both receptors in the absence presence of ligands. (c) 1,25D3 induced conformational changes of the RXR-VDR heterodimer complex bound by 9-cis-RA (Supplementary Tables 1b(iv) and 1c(iv)). (d) 9-cis-RA induced conformational changes of the RXR-VDR heterodimer complex when bound to 1,25D3 (Supplementary Tables 1b(v) and 1c(v)).
Figure 2
Figure 2. Ligand-induced domain-domain interactions within the RXR-VDR heterodimer complex
Differential HDX data mapped onto RXR-VDR docking model demonstrates (a) 1,25D3 (Supplementary Tables 1b(ii),and 1c(ii)) (b) 9-cis-RA (Supplementary Tables 1b(iii) and 1c(iii)) induced conformational changes of the RXR-VDR heterodimer complex as shown by comparing the deuterium incorporation of both receptors in the absence presence of ligands. (c) 1,25D3 induced conformational changes of the RXR-VDR heterodimer complex bound by 9-cis-RA (Supplementary Tables 1b(iv) and 1c(iv)). (d) 9-cis-RA induced conformational changes of the RXR-VDR heterodimer complex when bound to 1,25D3 (Supplementary Tables 1b(v) and 1c(v)).
Figure 2
Figure 2. Ligand-induced domain-domain interactions within the RXR-VDR heterodimer complex
Differential HDX data mapped onto RXR-VDR docking model demonstrates (a) 1,25D3 (Supplementary Tables 1b(ii),and 1c(ii)) (b) 9-cis-RA (Supplementary Tables 1b(iii) and 1c(iii)) induced conformational changes of the RXR-VDR heterodimer complex as shown by comparing the deuterium incorporation of both receptors in the absence presence of ligands. (c) 1,25D3 induced conformational changes of the RXR-VDR heterodimer complex bound by 9-cis-RA (Supplementary Tables 1b(iv) and 1c(iv)). (d) 9-cis-RA induced conformational changes of the RXR-VDR heterodimer complex when bound to 1,25D3 (Supplementary Tables 1b(v) and 1c(v)).
Figure 3
Figure 3. The interactions between RXR and VDR when bound to DNA
Differential HDX data mapped onto RXR-VDR docking model of DBD and LBD domains when bound to different ligands and DNA response elements. (a) The interactions between RXR and VDR on VDREdr3 in absence of ligands (Supplementary Tables 1b(vi) and 1c(vi)). (b) The interactions between RXR and VDR on VDREdr3 in presence of 1,25D3 only (Supplementary Tables 1b(vii) and 1c(vii)). (c) The interactions between RXR and VDR on VDREdr3 in presence of 1,25D3 and 9-cis-RA (Supplementary Tables 1b(viii) and 1c(viii)). (d) The interactions between RXR and VDR on Cyp24vdre in presence of 1,25D3 and 9-cis-RA (Supplementary Tables 1b(ix) and 1c(ix)).
Figure 3
Figure 3. The interactions between RXR and VDR when bound to DNA
Differential HDX data mapped onto RXR-VDR docking model of DBD and LBD domains when bound to different ligands and DNA response elements. (a) The interactions between RXR and VDR on VDREdr3 in absence of ligands (Supplementary Tables 1b(vi) and 1c(vi)). (b) The interactions between RXR and VDR on VDREdr3 in presence of 1,25D3 only (Supplementary Tables 1b(vii) and 1c(vii)). (c) The interactions between RXR and VDR on VDREdr3 in presence of 1,25D3 and 9-cis-RA (Supplementary Tables 1b(viii) and 1c(viii)). (d) The interactions between RXR and VDR on Cyp24vdre in presence of 1,25D3 and 9-cis-RA (Supplementary Tables 1b(ix) and 1c(ix)).
Figure 3
Figure 3. The interactions between RXR and VDR when bound to DNA
Differential HDX data mapped onto RXR-VDR docking model of DBD and LBD domains when bound to different ligands and DNA response elements. (a) The interactions between RXR and VDR on VDREdr3 in absence of ligands (Supplementary Tables 1b(vi) and 1c(vi)). (b) The interactions between RXR and VDR on VDREdr3 in presence of 1,25D3 only (Supplementary Tables 1b(vii) and 1c(vii)). (c) The interactions between RXR and VDR on VDREdr3 in presence of 1,25D3 and 9-cis-RA (Supplementary Tables 1b(viii) and 1c(viii)). (d) The interactions between RXR and VDR on Cyp24vdre in presence of 1,25D3 and 9-cis-RA (Supplementary Tables 1b(ix) and 1c(ix)).
Figure 3
Figure 3. The interactions between RXR and VDR when bound to DNA
Differential HDX data mapped onto RXR-VDR docking model of DBD and LBD domains when bound to different ligands and DNA response elements. (a) The interactions between RXR and VDR on VDREdr3 in absence of ligands (Supplementary Tables 1b(vi) and 1c(vi)). (b) The interactions between RXR and VDR on VDREdr3 in presence of 1,25D3 only (Supplementary Tables 1b(vii) and 1c(vii)). (c) The interactions between RXR and VDR on VDREdr3 in presence of 1,25D3 and 9-cis-RA (Supplementary Tables 1b(viii) and 1c(viii)). (d) The interactions between RXR and VDR on Cyp24vdre in presence of 1,25D3 and 9-cis-RA (Supplementary Tables 1b(ix) and 1c(ix)).
Figure 4
Figure 4. Ligand dependency of SRC1-RID binding to RXR-VDR heterdimer complex
Differential HDX data mapped onto RXR-VDR docking model of LBD domains in presence of various ligands and SRC1-RID. (a) In presence of both 1,25D3 and 9-cis-RA (Supplementary Tables 1b(x) and 1c(x)). (b) In presence of 1,25D3 only (Supplementary Tables 1b(xi) and 1c(xi)). (c) In presence of 9-cis-RA only (Supplementary Tables 1b(xii) and 1c(xii)). (d) In absence of both ligands (Supplementary Tables 1b(xiii) and 1c(xiii)). Comparison of differential HDX dynamics of the peptides (residues 411-419 and 412-419) from VDR helix 12 (e) and the peptides (residues 271-279 and 433-438) from RXR H3 and H10-11 (f) induced by SRC1-RID binding. Solid lines represent the deuterium incorporation of the peptides from the heterodimer bound to both 1,25D3 and 9cis-RA in the presence or absence of SRC1-RID and the dotted lines represent the deuterium incorporation of the peptides from the heterodimer bound to either 1,25D3 (e) or 9-cis-RA (f) only in the presence or absence of SRC1-RID. The value in parentheses represents the charge state of the peptide ions. Data were the mean ± s.d. of triplicate individual measurements.
Figure 4
Figure 4. Ligand dependency of SRC1-RID binding to RXR-VDR heterdimer complex
Differential HDX data mapped onto RXR-VDR docking model of LBD domains in presence of various ligands and SRC1-RID. (a) In presence of both 1,25D3 and 9-cis-RA (Supplementary Tables 1b(x) and 1c(x)). (b) In presence of 1,25D3 only (Supplementary Tables 1b(xi) and 1c(xi)). (c) In presence of 9-cis-RA only (Supplementary Tables 1b(xii) and 1c(xii)). (d) In absence of both ligands (Supplementary Tables 1b(xiii) and 1c(xiii)). Comparison of differential HDX dynamics of the peptides (residues 411-419 and 412-419) from VDR helix 12 (e) and the peptides (residues 271-279 and 433-438) from RXR H3 and H10-11 (f) induced by SRC1-RID binding. Solid lines represent the deuterium incorporation of the peptides from the heterodimer bound to both 1,25D3 and 9cis-RA in the presence or absence of SRC1-RID and the dotted lines represent the deuterium incorporation of the peptides from the heterodimer bound to either 1,25D3 (e) or 9-cis-RA (f) only in the presence or absence of SRC1-RID. The value in parentheses represents the charge state of the peptide ions. Data were the mean ± s.d. of triplicate individual measurements.
Figure 4
Figure 4. Ligand dependency of SRC1-RID binding to RXR-VDR heterdimer complex
Differential HDX data mapped onto RXR-VDR docking model of LBD domains in presence of various ligands and SRC1-RID. (a) In presence of both 1,25D3 and 9-cis-RA (Supplementary Tables 1b(x) and 1c(x)). (b) In presence of 1,25D3 only (Supplementary Tables 1b(xi) and 1c(xi)). (c) In presence of 9-cis-RA only (Supplementary Tables 1b(xii) and 1c(xii)). (d) In absence of both ligands (Supplementary Tables 1b(xiii) and 1c(xiii)). Comparison of differential HDX dynamics of the peptides (residues 411-419 and 412-419) from VDR helix 12 (e) and the peptides (residues 271-279 and 433-438) from RXR H3 and H10-11 (f) induced by SRC1-RID binding. Solid lines represent the deuterium incorporation of the peptides from the heterodimer bound to both 1,25D3 and 9cis-RA in the presence or absence of SRC1-RID and the dotted lines represent the deuterium incorporation of the peptides from the heterodimer bound to either 1,25D3 (e) or 9-cis-RA (f) only in the presence or absence of SRC1-RID. The value in parentheses represents the charge state of the peptide ions. Data were the mean ± s.d. of triplicate individual measurements.
Figure 4
Figure 4. Ligand dependency of SRC1-RID binding to RXR-VDR heterdimer complex
Differential HDX data mapped onto RXR-VDR docking model of LBD domains in presence of various ligands and SRC1-RID. (a) In presence of both 1,25D3 and 9-cis-RA (Supplementary Tables 1b(x) and 1c(x)). (b) In presence of 1,25D3 only (Supplementary Tables 1b(xi) and 1c(xi)). (c) In presence of 9-cis-RA only (Supplementary Tables 1b(xii) and 1c(xii)). (d) In absence of both ligands (Supplementary Tables 1b(xiii) and 1c(xiii)). Comparison of differential HDX dynamics of the peptides (residues 411-419 and 412-419) from VDR helix 12 (e) and the peptides (residues 271-279 and 433-438) from RXR H3 and H10-11 (f) induced by SRC1-RID binding. Solid lines represent the deuterium incorporation of the peptides from the heterodimer bound to both 1,25D3 and 9cis-RA in the presence or absence of SRC1-RID and the dotted lines represent the deuterium incorporation of the peptides from the heterodimer bound to either 1,25D3 (e) or 9-cis-RA (f) only in the presence or absence of SRC1-RID. The value in parentheses represents the charge state of the peptide ions. Data were the mean ± s.d. of triplicate individual measurements.
Figure 4
Figure 4. Ligand dependency of SRC1-RID binding to RXR-VDR heterdimer complex
Differential HDX data mapped onto RXR-VDR docking model of LBD domains in presence of various ligands and SRC1-RID. (a) In presence of both 1,25D3 and 9-cis-RA (Supplementary Tables 1b(x) and 1c(x)). (b) In presence of 1,25D3 only (Supplementary Tables 1b(xi) and 1c(xi)). (c) In presence of 9-cis-RA only (Supplementary Tables 1b(xii) and 1c(xii)). (d) In absence of both ligands (Supplementary Tables 1b(xiii) and 1c(xiii)). Comparison of differential HDX dynamics of the peptides (residues 411-419 and 412-419) from VDR helix 12 (e) and the peptides (residues 271-279 and 433-438) from RXR H3 and H10-11 (f) induced by SRC1-RID binding. Solid lines represent the deuterium incorporation of the peptides from the heterodimer bound to both 1,25D3 and 9cis-RA in the presence or absence of SRC1-RID and the dotted lines represent the deuterium incorporation of the peptides from the heterodimer bound to either 1,25D3 (e) or 9-cis-RA (f) only in the presence or absence of SRC1-RID. The value in parentheses represents the charge state of the peptide ions. Data were the mean ± s.d. of triplicate individual measurements.
Figure 4
Figure 4. Ligand dependency of SRC1-RID binding to RXR-VDR heterdimer complex
Differential HDX data mapped onto RXR-VDR docking model of LBD domains in presence of various ligands and SRC1-RID. (a) In presence of both 1,25D3 and 9-cis-RA (Supplementary Tables 1b(x) and 1c(x)). (b) In presence of 1,25D3 only (Supplementary Tables 1b(xi) and 1c(xi)). (c) In presence of 9-cis-RA only (Supplementary Tables 1b(xii) and 1c(xii)). (d) In absence of both ligands (Supplementary Tables 1b(xiii) and 1c(xiii)). Comparison of differential HDX dynamics of the peptides (residues 411-419 and 412-419) from VDR helix 12 (e) and the peptides (residues 271-279 and 433-438) from RXR H3 and H10-11 (f) induced by SRC1-RID binding. Solid lines represent the deuterium incorporation of the peptides from the heterodimer bound to both 1,25D3 and 9cis-RA in the presence or absence of SRC1-RID and the dotted lines represent the deuterium incorporation of the peptides from the heterodimer bound to either 1,25D3 (e) or 9-cis-RA (f) only in the presence or absence of SRC1-RID. The value in parentheses represents the charge state of the peptide ions. Data were the mean ± s.d. of triplicate individual measurements.
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