Evidence map›Paper›PMID 24187139›Full record

ArticleThe Journal of biological chemistry2014

Defining the communication between agonist and coactivator binding in the retinoid X receptor α ligand binding domain.

Leeann J Boerma, Gang Xia, Cheng Qui, Bryan D Cox, Michael J Chalmers, Craig D Smith, Susan Lobo-Ruppert, Patrick R Griffin, Donald D Muccio, Matthew B Renfrow

Open access · hybridAbstract read
In one paragraph

Article in The Journal of biological chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
2.2field-weighted citation impact, top 12% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 52 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 5 institutions in 2 countries.

Leeann J BoermaFrom the Departments of Biochemistry and Molecular Genetics.
Gang Xia
Cheng Qui
Bryan D Cox
Michael J Chalmers
Craig D Smith
Susan Lobo-Ruppert
Patrick R Griffin
Donald D Muccio
Matthew B Renfrow
University of Alabama at Birmingham · USScripps Research Institute · USApplied Visions (United States) · USLaboratory of Molecular Genetics · PLWorld Vision · US

Funding

XRAY CRYSTALLOGRAPHYP30CA013148 · NCI · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI Robert S Welner · 1985 to 2026
$165.9M
UAB Rexinoids for Breast Cancer PreventionP50CA089019 · NCI · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI GRIZZLE, WILLIAM E. · 2000 to 2011
$26.0M
University of Alabama at Birmingham's Diabetes Research CenterP30DK079626 · NIDDK · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI Kirk Michael Habegger · 2013 to 2026
$19.5M
Development of H/D exchange technology for the study of large protein complexesR01GM084041 · NIGMS · SCRIPPS FLORIDA · PI GRIFFIN, PATRICK ROBERT · 2009 to 2012
$1.6M
9.4 Tesla Fourier Transform Mass SpectrometerS10RR017261 · NCRR · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI BARNES, STEPHEN · 2002 to 2002
$1.5M
Acquisition of a LTQ/Orbitrap MS to advance the study of protein dynamicsS10RR027270 · NCRR · SCRIPPS RESEARCH INSTITUTE, THE · PI GRIFFIN, PATRICK ROBERT · 2010 to 2010
$500k
NCI NIH HHS 2 P50 CA089019NCI NIH HHS 5 P50 CA089019NCI NIH HHS P30 CA013148NCI NIH HHS P50 CA089019NCRR NIH HHS RR17261NCRR NIH HHS S10 RR017261NCRR NIH HHS S10 RR027270NIDDK NIH HHS P30 DK079626NIGMS NIH HHS R01 GM084041
6 · The paper itself

Abstract

Retinoid X receptors (RXRs) are obligate partners for several other nuclear receptors, and they play a key role in several signaling processes. Despite being a promiscuous heterodimer partner, this nuclear receptor is a target of therapeutic intervention through activation using selective RXR agonists (rexinoids). Agonist binding to RXR initiates a large conformational change in the receptor that allows for coactivator recruitment to its surface and enhanced transcription. Here we reveal the structural and dynamical changes produced when a coactivator peptide binds to the human RXRα ligand binding domain containing two clinically relevant rexinoids, Targretin and 9-cis-UAB30. Our results show that the structural changes are very similar for each rexinoid and similar to those for the pan-agonist 9-cis-retinoic acid. The four structural changes involve key residues on helix 3, helix 4, and helix 11 that move from a solvent-exposed environment to one that interacts extensively with helix 12. Hydrogen-deuterium exchange mass spectrometry reveals that the dynamics of helices 3, 11, and 12 are significantly decreased when the two rexinoids are bound to the receptor. When the pan-agonist 9-cis-retinoic acid is bound to the receptor, only the dynamics of helices 3 and 11 are reduced. The four structural changes are conserved in all x-ray structures of the RXR ligand-binding domain in the presence of agonist and coactivator peptide. They serve as hallmarks for how RXR changes conformation and dynamics in the presence of agonist and coactivator to initiate signaling.

Indexed as

AlitretinoinAmino Acid SequenceBexaroteneBinding SitesCrystallography, X-RayFatty Acids, UnsaturatedHumansLigandsModels, MolecularMolecular Sequence DataMolecular StructureNaphthalenesNuclear Receptor Coactivator 2Protein BindingProtein ConformationProtein MultimerizationAlitretinoinBexaroteneFatty Acids, UnsaturatedLigandsNaphthalenesNuclear Receptor Coactivator 2Retinoid X Receptor alphaTetrahydronaphthalenesTretinoinUAB 309-cis-UAB30AgonistsNuclear ReceptorsProtein DynamicsRetinoidRXR ReceptorStructural BiologyTargretinX-ray Crystallography

Identifiers

PMID24187139
PMCPMC3887207
OpenAlexW2086216924

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.