PDBsum entry 1kv6

Gene regulation

PDB id: 1kv6

Contents

Protein chains

222 a.a. *

11 a.a. *

Ligands

HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-GLU

Waters ×31

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural and functional evidence for ligand-Independent transcriptional activation by the estrogen-Related receptor 3.

Authors

H.Greschik, J.M.Wurtz, S.Sanglier, W.Bourguet, A.Van dorsselaer, D.Moras, J.P.Renaud.

Ref.

Mol Cell, 2002, 9, 303-313. [DOI no: 10.1016/S1097-2765(02)00444-6]

PubMed id

11864604

Abstract

The crystal structure of the ligand binding domain (LBD) of the estrogen-related receptor 3 (ERR3) complexed with a steroid receptor coactivator-1 (SRC-1) peptide reveals a transcriptionally active conformation in absence of any ligand. The structure explains why estradiol does not bind ERRs with significant affinity. Docking of the previously reported ERR antagonists, diethylstilbestrol and 4-hydroxytamoxifen, requires structural rearrangements enlarging the ligand binding pocket that can only be accommodated with an antagonist LBD conformation. Mutant receptors in which the ligand binding cavity is filled up by bulkier side chains still interact with SRC-1 in vitro and are transcriptionally active in vivo, but are no longer efficiently inactivated by diethylstilbestrol or 4-hydroxytamoxifen. These results provide structural and functional evidence for ligand-independent transcriptional activation by ERR3.

Figure 2.
Figure 2. Schematic Representation of the Ligand binding Pocket of the ERR3 LBD(A) In the crystal structure, the positions of all shown side chains are well defined, with the exception of that of E275, which exhibits high temperature factors. All atoms are colored according to the following code: carbon, gray; oxygen, red; nitrogen, blue; sulfur, yellow.(B) View as in (A) with E2 docked into the empty ligand binding cavity of ERR3. The position of E2 results from the superposition of the ERR3 LBD and the ERα LBD/E2 complex. Steric interference with the D-ring of E2 is mainly due to the presence of F435 (L525 in hERα) and L345 (I424 in hERα) in ERR3.(C) Schematic comparison of amino acid residues that form the ligand binding pocket in hERR3 with the corresponding residues of hERR2, hERR1, and hERα. Residues that are conserved among all four receptors are depicted in yellow, and those conserved among the ERR isotypes are colored in blue. Amino acids of hERα that according to our modeling studies allow the binding of E2 to ERs but not to ERRs are highlighted in red. Important isotype-specific amino acid differences are colored in green.

Figure 4.
Figure 4. In Vitro Interaction Between Wild-Type or Mutant LBDs of ERR3 and the RID of SRC-1Two micrograms (about 70 pmol) of partially purified His-tagged ERR3 LBD was preincubated for 10 min on ice with 4 μg (about 100 pmol) of GST-tagged SRC-1 RID or GST in the absence (A) or in the presence ([B] and [C]) of 10^−4 M 4-OHT or 10^−4 M DES. Complexes were separated on native polyacrylamide gradient gels.

The above figures are reprinted by permission from Cell Press: Mol Cell (2002, 9, 303-313) copyright 2002.

Secondary reference #1

Title

Molecular basis of agonism and antagonism in the oestrogen receptor.

Authors

A.M.Brzozowski, A.C.Pike, Z.Dauter, R.E.Hubbard, T.Bonn, O.Engström, L.Ohman, G.L.Greene, J.A.Gustafsson, M.Carlquist.

Ref.

Nature, 1997, 389, 753-758. [DOI no: 10.1038/39645]

PubMed id

9338790

Figure 2.
Figure 2 Agonist and antagonist binding modes. a, The 3.1-Å resolution, six-fold averaged electron-density map (using model phases) for the ER LBD-E[2] complex. b, The experimental, 2.6-Å resolution electron-density map for the ER LBD-RAL complex after DMMULTI multicrystal averaging. In both cases, the map is contoured at 1 and overlaid on the final refined models. c, d, Schematic representation of the interactions made by E[2] (c) and RAL (d) within the binding cavity. Residues that interact with ligand and/or line the cavity are shown in theirapproximate positions. Those that make direct hydrogen bonds are depictedin ball-and-stick style with broken lines between the interacting atoms.The hydrogen-bond distances shown are averaged between the six (E[2]) or two (RAL) monomers. The atom names and ring nomenclature of E[2] are also given.

Figure 3.
Figure 3 Positioning of helix H12. Position is shown in a, the ER LBD-E[2] complex; and b, the ER LBD-RAL complex. H12 is drawn as a cylinder and coloured blue (E[2] complex) or green (RAL complex). The remainder of the ER LBD is shown in red. Dotted lines indicate unmodelled regions of the structures. Hydrophobic residues located in the groove between H3 and H5 (yellow) and Lys 362 (K362, pink) are depicted in space-filling form. The locations of Asp 538, Glu 542 and Asp 545 are highlighted (brown spheres) along with the helices that interact with H12 in the two complexes.

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd

Secondary reference #2

Title

The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen.

Authors

A.K.Shiau, D.Barstad, P.M.Loria, L.Cheng, P.J.Kushner, D.A.Agard, G.L.Greene.

Ref.

Cell, 1998, 95, 927-937. [DOI no: 10.1016/S0092-8674(00)81717-1]

PubMed id

9875847

Figure 1.
Figure 1. Views of the Electron Density of the DES-ERα LBD-GRIP1 NR Box II Peptide Complex and of the OHT-ERα LBD Complex(A) A view of a 2F[o]−F[c] electron density map of the DES-LBD-peptide complex calculated at 2.03 Šresolution and contoured at 1.0 σ showing the GRIP1 NR box II interaction with the LBD. The peptide was omitted from the model prior to map calculation. Ile-689 from the peptide and two of the three receptor residues with which it interacts (Glu-542 and Leu-539) are labeled. Asp-538 has been omitted for clarity. The hydrogen bonds between the γ-carboxylate of Glu-542 and the amides of residues 689 and 690 of the peptide are depicted as dashed orange bonds.(B) A view of a 2F[o]−F[c] electron density map of the OHT-LBD complex calculated at 1.90 Šresolution and contoured at 1.0 σ showing the N-terminal region of helix 12. The dashed orange bonds depict the water-mediated hydrogen bond network between the imidazole ring of His-377, the γ-carboxylate of Glu-380, and the amide of Tyr-537. The three labeled residues (Glu-380, Leu-536, and Tyr-537) interact with each other through van der Waals contacts and/or hydrogen bonds.

Figure 4.
Figure 4. DES Interactions with the LBD (A) and OHT Interactions with the LBD (B)Residues that interact with the ligands are drawn at approximately their true positions. The residues that form van der Waals contacts with ligand are depicted as labeled arcs with radial spokes that point towards the ligand atoms with which they interact. The residues that hydrogen bond to ligand are shown in ball-and-stick representation. Hydrogen bonds are represented as dashed cyan lines; the distance of each bond is given. The ligand rings and the individual ligand atoms are labeled.

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #3

Title

X-Ray structure of the orphan nuclear receptor rorbeta ligand-Binding domain in the active conformation.

Authors

C.Stehlin, J.M.Wurtz, A.Steinmetz, E.Greiner, R.Schüle, D.Moras, J.P.Renaud.

Ref.

EMBO J, 2001, 20, 5822-5831. [DOI no: 10.1093/emboj/20.21.5822]

PubMed id

11689423

Figure 2.
Figure 2 Schematic representation of the rROR LBD in complex with stearate (ball-and-stick) and a SRC-1 peptide (ribbon representation). The kink in H10 has been emphasized by breaking H10 into two segments.

Figure 5.
Figure 5 Homology modeling of ROR , ROR and DHR3 LBDs, showing the non-conserved residues affecting the pocket's shape. Figures 2, 3A, 4 and 5 were prepared with SETOR (Evans, 1993).

The above figures are reproduced from the cited reference which is an Open Access publication published by Macmillan Publishers Ltd

Secondary reference #4

Title

Structural studies on nuclear receptors.

Authors

J.P.Renaud, D.Moras.

Ref.

Cell Mol Life Sci, 2000, 57, 1748-1769.

PubMed id

11130180