PDB-4n5g: Crystal Structure of RXRa LBD complexed with a synthetic modulato...

ID or keywords:

Entry

Database: PDB / ID: 4n5g

Title

Crystal Structure of RXRa LBD complexed with a synthetic modulator K8012

Components

Retinoic acid receptor RXR-alpha

Keywords

SIGNALING PROTEIN / Retinoid X receptor-alpha nuclear receptor / Nucleus

Function / homology

Function and homology information

positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex ...positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.11 Å

Authors

Aleshin, A.E. / Su, Y. / Zhang, X. / Liddington, R.C.

Citation

Journal: Chem.Biol. / Year: 2014
Title: Sulindac-Derived RXR alpha Modulators Inhibit Cancer Cell Growth by Binding to a Novel Site.
Authors: Chen, L. / Wang, Z.G. / Aleshin, A.E. / Chen, F. / Chen, J. / Jiang, F. / Alitongbieke, G. / Zeng, Z. / Ma, Y. / Huang, M. / Zhou, H. / Cadwell, G. / Zheng, J.F. / Huang, P.Q. / Liddington, ...

History

Deposition	Oct 9, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 11, 2014	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4n5g.cif.gz	343.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4n5g.ent.gz	280.6 KB	Display	PDB format
PDBx/mmJSON format	4n5g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4n5g_validation.pdf.gz	994 KB	Display	wwPDB validaton report
Full document	4n5g_full_validation.pdf.gz	1004.7 KB	Display
Data in XML	4n5g_validation.xml.gz	32.6 KB	Display
Data in CIF	4n5g_validation.cif.gz	45 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n5/4n5g ftp://data.pdbj.org/pub/pdb/validation_reports/n5/4n5g	HTTPS FTP

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Related structure data

Related structure data	4n8rC 1g1uS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4n8r-d 6jno-d 7cfo-d 5tbp-d 5zqu-d 6kyv-4 3nsp-1 6kyv-3 3nsq-1 5jc3-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#155 - Nov 2012 Vitamin D Receptor similarity (20) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (7) #122 - Feb 2010 Enhanceosome similarity (3) #92 - Aug 2007 Anabolic Steroids similarity (2) #37 - Jan 2003 Serum Albumin similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1)

Deposited unit

A: Retinoic acid receptor RXR-alpha

B: Retinoic acid receptor RXR-alpha

C: Retinoic acid receptor RXR-alpha

D: Retinoic acid receptor RXR-alpha

hetero molecules

110 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	46.585, 98.830, 110.579
Angle α, β, γ (deg.)	90.00, 99.02, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha Mass: 27269.514 Da / Num. of mol.: 4 / Fragment: ligand binding domain (UNP residues 223-462) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P19793
#2: Chemical	ChemComp-K09 / 5-(2-{(1Z)-5-fluoro-2-methyl-1-[4-(propan-2-yl)benzylidene]-1H-inden-3-yl}ethyl)-1H-tetrazole Mass: 374.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₃H₂₃FN₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG3330, 0.2M Na Acetate, 100 mM NaCl, 20 mM Tris-Cl, 0.5 mM ligand K-8012, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 200 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2013 / Details: mirrors
Radiation	Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.11→37.242 Å / Num. all: 56915 / Num. obs: 48947 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / B_iso Wilson estimate: 40.3 Å² / R_merge(I) obs: 0.079 / Net I/σ(I): 8.1
Reflection shell	Resolution: 2.11→2.17 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 1.6 / % possible all: 50

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1G1U

1g1u

Resolution: 2.11→37 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 25.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2468	2144	4.94 %	random
R_work	0.1989	-	-	-
obs	0.2012	43378	87.77 %	-
all	-	49423	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.11→37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6390	0	56	276	6722

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6662
X-RAY DIFFRACTION	f_angle_d	0.728	9023
X-RAY DIFFRACTION	f_dihedral_angle_d	12.309	2507
X-RAY DIFFRACTION	f_chiral_restr	0.028	1023
X-RAY DIFFRACTION	f_plane_restr	0.003	1150

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.11-2.225	0.2798	163	0.2559	2703	X-RAY DIFFRACTION	86
2.225-2.2512	0.3311	144	0.2574	2860	X-RAY DIFFRACTION	93
2.2512-2.2786	0.2755	131	0.2574	2846	X-RAY DIFFRACTION	91
2.2786-2.3075	0.3466	143	0.2409	2801	X-RAY DIFFRACTION	88
2.3075-2.3378	0.301	150	0.2465	2855	X-RAY DIFFRACTION	91
2.3378-2.3698	0.3023	146	0.2321	2844	X-RAY DIFFRACTION	92
2.3698-2.4037	0.2662	154	0.2367	2768	X-RAY DIFFRACTION	89
2.4037-2.4396	0.3411	144	0.2432	2766	X-RAY DIFFRACTION	88
2.4396-2.4777	0.3461	143	0.2507	2774	X-RAY DIFFRACTION	88
2.4777-2.5183	0.3185	131	0.2366	2785	X-RAY DIFFRACTION	88
2.5183-2.5617	0.3022	129	0.2407	2429	X-RAY DIFFRACTION	78
2.5617-2.6083	0.2609	129	0.2283	2803	X-RAY DIFFRACTION	89
2.6083-2.6584	0.292	172	0.2181	2872	X-RAY DIFFRACTION	94
2.6584-2.7127	0.3222	136	0.2147	2820	X-RAY DIFFRACTION	89
2.7127-2.7716	0.2486	132	0.2087	2889	X-RAY DIFFRACTION	91
2.7716-2.8361	0.2498	159	0.2049	2848	X-RAY DIFFRACTION	91
2.8361-2.907	0.2753	138	0.2115	2795	X-RAY DIFFRACTION	87
2.907-2.9856	0.2745	159	0.2144	2711	X-RAY DIFFRACTION	89
2.9856-3.0734	0.3129	144	0.2109	2677	X-RAY DIFFRACTION	85
3.0734-3.1725	0.2764	140	0.2293	2507	X-RAY DIFFRACTION	81
3.1725-3.2858	0.2831	152	0.2139	2900	X-RAY DIFFRACTION	92
3.2858-3.4173	0.2422	158	0.2016	2826	X-RAY DIFFRACTION	90
3.4173-3.5727	0.2743	152	0.1919	2731	X-RAY DIFFRACTION	88
3.5727-3.7609	0.2233	153	0.1781	2720	X-RAY DIFFRACTION	88
3.7609-3.9963	0.2342	115	0.1703	2649	X-RAY DIFFRACTION	84
3.9963-4.3044	0.1964	136	0.1619	2488	X-RAY DIFFRACTION	80
4.3044-4.7368	0.1813	145	0.1662	2780	X-RAY DIFFRACTION	88
4.7368-5.4205	0.2298	135	0.1815	2659	X-RAY DIFFRACTION	86
5.4205-6.8224	0.2592	118	0.2169	2573	X-RAY DIFFRACTION	81
6.8224-37.2469	0.1657	137	0.1764	2790	X-RAY DIFFRACTION	89

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	8.7931	0.5017	4.2497	3.9395	1.4505	6.5078	-0.6798	0.9084	0.8421	-0.5011	0.2573	0.1847	-0.9409	0.1316	0.4	0.4168	-0.0658	-0.0186	0.3328	0.0988	0.355	14.9926	19.0508	28.0474
2	3.0079	0.6029	-0.0765	2.7778	0.2721	2.8714	-0.0617	0.1698	0.2247	0.0925	-0.0197	0.217	-0.0975	-0.2168	0.0995	0.1781	0.0365	-0.031	0.1779	0.0037	0.2183	8.9083	10.8328	39.8699
3	1.3648	0.8404	1.8728	1.2222	0.7376	5.0268	-0.0547	0.1227	0.2026	-0.2626	-0.0779	0.075	-0.1951	-0.379	0.0695	0.2341	0.0648	0.034	0.2653	-0.0216	0.263	4.0488	6.9731	32.539
4	4.1755	-1.6117	-0.9928	5.0793	1.6542	5.1928	0.1003	-0.191	-0.0752	0.1105	0.0058	-0.2609	0.34	0.3703	-0.1427	0.5031	-0.0274	-0.0421	0.2297	0.1051	0.2869	15.0115	-18.5538	51.6964
5	3.7377	-0.9367	-1.4278	2.5816	1.5511	4.4633	-0.0326	0.5588	-0.2479	-0.1546	0.0075	-0.5534	0.6821	0.7143	0.0441	0.4157	0.157	0.0639	0.475	-0.0114	0.3789	27.8573	-10.4761	39.1991
6	3.7484	0.7671	0.6386	3.3621	-0.0973	3.4339	0.122	-0.1365	-0.0792	0.3962	-0.0209	-0.1595	0.3085	0.2728	-0.1025	0.2637	0.0758	-0.0298	0.1628	0.0047	0.2117	17.9166	-1.9662	50.9689
7	2.6392	-0.0579	-0.7174	3.6751	5.7668	9.2003	-0.0551	0.4402	-0.2344	0.6134	0.1335	-0.3447	0.2563	0.5245	0.0269	0.9828	0.432	-0.2312	0.7108	-0.2705	0.86	23.8714	-29.3676	27.9818
8	1.3469	-0.5281	-1.0468	3.0461	1.0457	2.6348	-0.1527	0.8411	-0.0611	-1.5124	-0.0762	0.3832	-1.1041	0.2884	0.2697	1.1897	-0.1369	0.0008	0.9177	0.199	0.7656	5.3033	2.9226	-3.0615
9	1.434	1.5392	0.3955	3.8819	1.1332	2.7889	-0.4148	0.3801	0.176	-0.7763	0.2277	0.1385	-0.3936	-0.1032	0.1971	0.4079	-0.0298	-0.0543	0.4053	0.11	0.3309	-1.6193	3.2374	4.1217
10	3.9224	-0.6682	-0.2131	3.0533	-0.2955	3.7344	-0.0207	0.34	0.3829	-0.42	0.1036	-0.3989	-0.0634	0.7132	-0.0536	0.3652	-0.0554	0.0521	0.4625	-0.0269	0.2729	10.6255	-8.4873	3.7079
11	5.5519	0.4218	-0.1793	2.2085	4.2863	8.5905	0.2157	0.2878	0.1704	-0.5778	-0.5354	-0.0424	-0.6412	-0.1205	0.2358	0.594	-0.0286	-0.0282	0.431	0.1258	0.4187	18.6727	16.0621	19.0677
12	3.2344	0.1279	-1.8702	3.1959	1.5837	7.111	0.0748	0.2079	-0.5441	-0.0556	0.0326	-0.2693	1.2631	0.3491	-0.044	0.6911	0.2067	-0.1644	0.4898	-0.1402	0.4805	16.689	-33.2437	21.903
13	3.5902	2.3464	-2.5048	3.5161	0.4661	3.7499	-0.5185	-0.6879	-0.3368	0.0392	0.256	0.0523	0.6509	0.0048	0.2229	0.6514	0.1791	-0.0801	0.4331	-0.0385	0.3277	1.1079	-27.8994	22.9062
14	0.9361	0.1548	1.0235	0.7488	-0.0274	2.3195	0.0962	0.1663	-0.2986	-0.1206	0.0598	-0.0218	0.2538	0.1464	-0.1526	0.3886	0.0288	-0.0158	0.2787	-0.0663	0.3023	5.0709	-23.8929	17.157

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 263:301)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 302:405)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 406:458)
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESID 231:302)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 303:359)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 360:437)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 438:458)
8	X-RAY DIFFRACTION	8	(CHAIN C AND RESID 231:264)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 265:301)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 302:437)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 438:458)
12	X-RAY DIFFRACTION	12	(CHAIN D AND RESID 263:301)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 302:333)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 334:458)

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