249,324
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

3KMZ|pdb_00003kmz

Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment

PDB DOI: https://doi.org/10.2210/pdb3KMZ/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-11 Released: 2010-06-02
Deposition Author(s): Bourguet, W.,le Maire, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model:experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

A unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor.

le Maire, A., Teyssier, C., Erb, C., Grimaldi, M., Alvarez, S., de Lera, A.R., Balaguer, P., Gronemeyer, H., Royer, C.A., Germain, P., Bourguet, W.

(2010) Nat Struct Mol Biol 17: 801-807

PubMed: 20543827 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.1855
Primary Citation of Related Structures:
3KMR,3KMZ

PubMed Abstract:
In the absence of ligand, some nuclear receptors, including retinoic acid receptor (RAR), act as transcriptional repressors by recruiting corepressor complexes to target genes. This constitutive repression is crucial in metazoan reproduction, development and homeostasis. However, its specific molecular determinants had remained obscure. Using structural, biochemical and cell-based assays, we show that the basal repressive activity of RAR is conferred by an extended beta-strand that forms an antiparallel beta-sheet with specific corepressor residues. Agonist binding induces a beta-strand-to-alpha-helix transition that allows for helix H11 formation, which in turn provokes corepressor release, repositioning of helix H12 and coactivator recruitment. Several lines of evidence suggest that this structural switch could be implicated in the intrinsic repressor function of other nuclear receptors. Finally, we report on the molecular mechanism by which inverse agonists strengthen corepressor interaction and enhance gene silencing by RAR.

Organizational Affiliation

Institut National de la Santé et de la Recherche Médicale, U554, Montpellier, France.

Macromolecule Content

Total Structure Weight: 66.07 kDa
Atom Count: 4,262
Modeled Residue Count: 480
Deposited Residue Count: 570
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor alpha	A [auth B], C [auth A]	266	Homo sapiens	Mutation(s): 0 Gene Names: NR1B1, RARA
UniProt & NIH Common Fund Data Resources
Find proteins for P10276 (Homo sapiens) Explore P10276 Go to UniProtKB: P10276
PHAROS: P10276 GTEx: ENSG00000131759
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10276
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor corepressor 1	B [auth C], D	19	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75376 (Homo sapiens) Explore O75376 Go to UniProtKB: O75376
PHAROS: O75376 GTEx: ENSG00000141027
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75376
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EQO Query on EQO Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain J [auth A] MOL2 format, chain E [auth B] MOL2 format, chain J [auth A] mmCIF format, chain E [auth B] mmCIF format, chain J [auth A]	E [auth B], J [auth A]	4-{(E)-2-[5,5-dimethyl-8-(phenylethynyl)-5,6-dihydronaphthalen-2-yl]ethenyl}benzoic acid C₂₉ H₂₄ O₂ YCADIXLLWMXYKW-CMDGGOBGSA-N		Interactions Focus chain E [auth B] Focus chain J [auth A] Interactions & Density Focus chain E [auth B] Focus chain J [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B] G [auth B] H [auth B] I [auth B] K [auth A] F [auth B], G [auth B], H [auth B], I [auth B], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	B [auth C], D	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
EQO	BindingDB: 3KMZ	IC50: 114 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.230 (Depositor), 0.230 (DCC)
R-Value Work: 0.172 (Depositor), 0.170 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.831	α = 90
b = 105.625	β = 89.92
c = 53.382	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-06-02

Deposition Author(s):

Bourguet, W.

le Maire, A.

Revision History (Full details and data files)

Version 1.0: 2010-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-22
Changes: Data collection
Version 1.4: 2024-11-20
Changes: Structure summary