PDBsum entry 1fby

Transcription

PDB id: 1fby

Contents

Protein chains

217 a.a. *

Ligands

9CR ×2

Waters ×203

* Residue conservation analysis

PDB id:

1fby

Name:

Transcription

Title:

Crystal structure of the human rxr alpha ligand binding domain bound to 9-cis retinoic acid

Structure:

Retinoic acid receptor rxr-alpha. Chain: a, b. Fragment: ligand binding domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.25Å R-factor: 0.228 R-free: 0.263

Authors:

P.F.Egea,A.Mitschler,N.Rochel,M.Ruff,P.Chambon,D.Moras

Key ref:

P.F.Egea et al. (2000). Crystal structure of the human RXRalpha ligand-binding domain bound to its natural ligand: 9-cis retinoic acid. EMBO J, 19, 2592-2601. PubMed id: 10835357 DOI: 10.1093/emboj/19.11.2592

Date:

17-Jul-00 Release date: 28-Jul-00

Protein chains

P19793  (RXRA_HUMAN) -  Retinoic acid receptor RXR-alpha from Homo sapiens

Seq: 462 a.a.

Struc: 217 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1093/emboj/19.11.2592

EMBO J 19:2592-2601 (2000)

PubMed id: 10835357

Crystal structure of the human RXRalpha ligand-binding domain bound to its natural ligand: 9-cis retinoic acid.

P.F.Egea, A.Mitschler, N.Rochel, M.Ruff, P.Chambon, D.Moras.

ABSTRACT

The pleiotropic effects of active retinoids are transduced by their cognate nuclear receptors, retinoid X receptors (RXRs) and retinoic acid receptors (RARs), which act as transcriptional regulators activated by two stereoisomers of retinoic acid (RA): 9-cis RA (9-cRA) and all-trans RA (a-tRA). Among nuclear receptors, RXR occupies a central position and plays a crucial role in many intracellular signalling pathways as a ubiquitous heterodimerization partner with numerous other members of this superfamily. Whereas RARs bind both isomers, RXRs exclusively bind 9-cRA. The crystal structure of the ligand-binding domain (LBD) of human RXRalpha bound to 9-cRA reveals the molecular basis of this ligand selectivity and allows a comparison of both apo and holo forms of the same nuclear receptor. In the crystal, the receptor is monomeric and exhibits a canonical agonist conformation without direct contacts between the ligand and the transactivation helix H12. Comparison with the unliganded RXRalpha LBD structure reveals the molecular mechanisms of ligand-induced conformational changes and allows us to describe at the atomic level how these changes generate the proper protein interface involved in nuclear receptor-coactivator interaction.

Selected figure(s)

Figure 2.
Figure 2 The bound 9-cRA in RXR and the comparison of the 9-cis retinoic binding modes in RXR and RAR . (A) Schematic drawing showing the interactions between the protein and the ligand molecule. Only contacts closer than 4.2 Å are indicated as dotted lines. The H3, H5, H7, H11 and -turn residues are indicated. (B) The ligand molecule shown in an F[o] – F[c] electron density omit map contoured at 2.0 SD. Water molecules are displayed as red spheres. Only residues closer than 4.2 Å are displayed. Direct and water-mediated hydrogen bond implicated residues are shown with green dotted lines. The same orientation is shown in both pictures. (C and D) The probe-occupied ligand cavities in RXR (C) and RAR (D) calculated by VOIDOO (Kleywegt and Jones, 1994) and MSMS with a probe radius of 1.4 Å are displayed in white using DINO (Philippsen, 1999). The occupation of both cavities by the 9-cRA ligand molecule is shown by transparency. Ligand atoms of 9-cRA are displayed in pale green and pink for carbon and oxygen atoms, respectively. (E) Superimposition of 9-cRA molecules from holo hRXR (yellow) and hRAR (red). (F) Relative orientations of 9-cRA and a-tRA molecules after superimposition of liganded hRXR and hRAR proteins. 9-cRA from liganded hRXR is coloured in red, 9-cRA from liganded hRAR is coloured in yellow and a-tRA molecule from liganded hRAR is coloured in green.

Figure 3.
Figure 3 The agonist conformation of transactivation helix H12 in the holo form. Docking of retinoid agonist (HX630) and antagonist (HX531) in hRXR LBP. (A and B) Agonist (HX600) and antagonist (HX531) compounds docked in the LBP of hRXR . Protein atoms are coloured in grey for carbon, blue for nitrogen, red for oxygen and yellow for sulfur. The oxygen and nitrogen atoms of docked compounds are depicted as red and blue spheres, respectively. 9-cRA is coloured in yellow, whereas docked ligands are colored in salmon. Cyan dotted lines represent the structurally conserved hydrogen interaction between the carboxylic moiety of ligands and residues Arg316 and Gln275 of the protein. Green dotted lines underline steric clashes through close interatomic contacts between ligand and protein atoms (the distance between consecutive dots is 0.5 Å). (C) Detailed stereoview of helix H12 contacts showing the exposed glutamic residues Glu453 and Glu456 involved in transactivation and the interactions stabilizing helix H12 in its agonist position. Helix H12 is depicted in red. 9-cRA ligand atoms are coloured in yellow for carbon and red for oxygen, respectively. Protein atoms are coloured in grey for carbon, blue for nitrogen, red for oxygen and yellow for sulfur. The protein backbone is coloured in blue. A water molecule is drawn as a red sphere and hydrogen bonds are depicted as green dotted lines. For the sake of clarity only a few side chains are labelled. (D) Schematic drawing of interactions stabilizing H12 in its agonist conformation. van der Waals interactions and hydrogen bonds are represented as dotted and continuous lines, respectively. A water molecule is referred to as w.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 2592-2601) copyright 2000.

Figures were selected by the author.