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Basic information

Entry
Database: PDB / ID: 6hn6
TitleA revisited version of the apo structure of the ligand-binding domain of the human nuclear receptor RXR-ALPHA
ComponentsRetinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / NUCLEAR RECEPTOR
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 shuttle / retinoic acid binding / TGFBR3 expression ...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 shuttle / retinoic acid binding / TGFBR3 expression / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / retinoic acid receptor signaling pathway / positive regulation of bone mineralization / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / 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 / sequence-specific DNA binding / transcription regulator complex / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.71 Å
AuthorsEberhardt, J. / McEwen, A.G. / Bourguet, W. / Moras, D. / Dejaegere, A.
Funding support France, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-10-BINF-003 France
French National Research AgencyANR-10-IDEX-0002-02 France
French National Research AgencyANR-10-INBS-05 France
French National Research AgencyANR-10-LABX-0030-INRT France
French National Research AgencyANR-IAB-2011-BIP:BIP France
Citation
Journal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: A revisited version of the apo structure of the ligand-binding domain of the human nuclear receptor retinoic X receptor alpha.
Authors: Eberhardt, J. / McEwen, A.G. / Bourguet, W. / Moras, D. / Dejaegere, A.
#1: Journal: Nature / Year: 1995
Title: Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-alpha.
Authors: Bourguet, W. / Ruff, M. / Chambon, P. / Gronemeyer, H. / Moras, D.
History
DepositionSep 14, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 20, 2019ID: 1LBD
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Mar 8, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1625
Polymers31,7021
Non-polymers2,4604
Water72140
1
A: Retinoic acid receptor RXR-alpha
hetero molecules

A: Retinoic acid receptor RXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,32310
Polymers63,4042
Non-polymers4,9198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+3/21
Unit cell
Length a, b, c (Å)110.800, 110.800, 109.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha


Mass: 31702.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HISTIDINE TAG PLUS DOMAIN D PLUS LIGAND-BINDING DOMAIN E
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: PET15-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19793
#2: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.45 M AMMONIUM CITRATE, 30 mM KCl, 4% GLYCEROL, 5 mM CHAPS, pH 7.0

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 9, 1994 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.71→7.99 Å / Num. obs: 9164 / % possible obs: 84.73 % / Redundancy: 4.8 % / Biso Wilson estimate: 66.28 Å2 / Net I/σ(I): 4.9
Reflection shellResolution: 2.71→3.03 Å / Num. unique obs: 2597 / % possible all: 83.03

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Phasing

PhasingMethod: MIR

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MLPHAREphasing
PDB_EXTRACT3.24data extraction
XDSMARXDSdata reduction
XSCALEMARSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.71→7.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.796 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.827 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.315
RfactorNum. reflection% reflectionSelection details
Rfree0.231 459 5.01 %RANDOM
Rwork0.173 ---
obs0.176 9164 84.7 %-
Displacement parametersBiso mean: 64.96 Å2
Baniso -1Baniso -2Baniso -3
1--3.8037 Å20 Å20 Å2
2---3.8037 Å20 Å2
3---7.6073 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 2.71→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 168 40 2078
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012103HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.092887HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d829SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it2103HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion17.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion295SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2458SEMIHARMONIC4
LS refinement shellResolution: 2.71→3.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.321 130 5.01 %
Rwork0.249 2467 -
all0.253 2597 -
obs--83.03 %
Refinement TLS params.

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

IDL11 (°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)
10.44351.7777-1.52012.4085-3.1120.8713-0.05450.03070.1136-0.04090.1304-0.2181-0.03750.116-0.0759-0.1406-0.12810.13110.09270.0747-0.012233.813882.187163.7381
23.3595-1.16910.71542.0394-0.20521.55070.01410.5650.1829-0.3119-0.1845-0.3085-0.29470.33530.17040.0321-0.05220.0645-0.02950.1151-0.114413.803179.450762.1177
31.5393-0.1099-0.1696-0.50320.16323.2183-0.18870.290.4252-0.07220.0301-0.3438-0.60350.27130.15860.0305-0.0904-0.0093-0.11130.09870.025117.912585.54473.9333
42.47141.64860.41521.2866-0.3192.58470.0243-0.05380.0902-0.02830.0818-0.24810.08080.6751-0.1061-0.1998-0.0550.04730.12780.1030.072233.271674.613173.8238
50.9539-0.9551.12130.44651.08444.2155-0.0195-0.05820.27040.01170.1416-0.2569-0.20880.201-0.122-0.0485-0.0561-0.0221-0.04720.073-0.000521.743682.834479.0425
64.8938-0.61691.83780.9723-0.0040.59640.04060.2340.0595-0.31650.04940.22-0.0914-0.1065-0.090.02590.0015-0.07720.03570.1303-0.0539-7.311279.260459.8918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|225 - A|242 }
2X-RAY DIFFRACTION2{ A|243 - A|340 }
3X-RAY DIFFRACTION3{ A|341 - A|375 }
4X-RAY DIFFRACTION4{ A|376 - A|407 }
5X-RAY DIFFRACTION5{ A|408 - A|435 }
6X-RAY DIFFRACTION6{ A|436 - A|462 }

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