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- PDB-6xwg: Crystal Structure of the Human RXR/RAR DNA-Binding Domain Heterod... -

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Basic information

Entry
Database: PDB / ID: 6xwg
TitleCrystal Structure of the Human RXR/RAR DNA-Binding Domain Heterodimer Bound to the Human RARb2 DR5 Response Element
Components
  • (RARb2 DR5 Response Element, ...) x 2
  • (Retinoic acid receptor ...) x 2
KeywordsTRANSCRIPTION / Protein-DNA complex / Nuclear Receptor
Function / homology
Function and homology information


Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / protein kinase B binding / negative regulation of granulocyte differentiation / growth plate cartilage development / glandular epithelial cell development ...Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / protein kinase B binding / negative regulation of granulocyte differentiation / growth plate cartilage development / glandular epithelial cell development / positive regulation of T-helper 2 cell differentiation / prostate gland development / positive regulation of transporter activity / negative regulation of cartilage development / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / regulation of hematopoietic progenitor cell differentiation / positive regulation of thyroid hormone receptor signaling pathway / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / outflow tract septum morphogenesis / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / response to vitamin A / limb development / apoptotic cell clearance / regulation of myelination / Signaling by Retinoic Acid / ureteric bud development / DNA binding domain binding / DNA-binding transcription repressor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / protein kinase A binding / nuclear steroid receptor activity / heterocyclic compound binding / LBD domain binding / positive regulation of interleukin-4 production / alpha-actinin binding / face development / germ cell development / negative regulation of type II interferon production / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor production / cellular response to estrogen stimulus / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of bone mineralization / response to retinoic acid / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to retinoic acid / positive regulation of cell cycle / hormone-mediated signaling pathway / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / response to cytokine / positive regulation of neuron differentiation / BMAL1:CLOCK,NPAS2 activates circadian expression / mRNA regulatory element binding translation repressor activity / negative regulation of miRNA transcription / peptide binding / Activation of gene expression by SREBF (SREBP) / liver development / hippocampus development / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / female pregnancy / neural tube closure / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / multicellular organism growth / regulation of synaptic plasticity / Nuclear Receptor transcription pathway / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / mRNA 5'-UTR binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / nervous system development
Similarity search - Function
: / : / Retinoic acid receptor / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...: / : / Retinoic acid receptor / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Retinoic acid receptor alpha / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMcEwen, A.G. / Poussin-Courmontagne, P. / Peluso-Iltis, C. / Rochel, N.
Funding support France, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV8-023 France
Fondation ARCSFI20121205585 France
French National Research AgencyFRISBI ANR-10-INBS-05 France
French National Research AgencyANR-10-LABX-0030-INRT France
French National Research AgencyANR-10-IDEX-0002-02 France
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR-RXR.
Authors: Osz, J. / McEwen, A.G. / Bourguet, M. / Przybilla, F. / Peluso-Iltis, C. / Poussin-Courmontagne, P. / Mely, Y. / Cianferani, S. / Jeffries, C.M. / Svergun, D.I. / Rochel, N.
History
DepositionJan 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RARb2 DR5 Response Element, 5'-3' strand
B: RARb2 DR5 Response Element, 3'-5' strand
C: Retinoic acid receptor RXR-alpha
D: Retinoic acid receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,17110
Polymers33,7824
Non-polymers3896
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-43 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.714, 56.714, 238.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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RARb2 DR5 Response Element, ... , 2 types, 2 molecules AB

#1: DNA chain RARb2 DR5 Response Element, 5'-3' strand


Mass: 6447.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain RARb2 DR5 Response Element, 3'-5' strand


Mass: 6438.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Retinoic acid receptor ... , 2 types, 2 molecules CD

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


Mass: 10262.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DNA-Binding Domain / Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19793
#4: Protein Retinoic acid receptor alpha / RAR-alpha / Nuclear receptor subfamily 1 group B member 1


Mass: 10633.478 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DNA-Binding Domain / Source: (gene. exp.) Homo sapiens (human) / Gene: RARA, NR1B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10276

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Non-polymers , 4 types, 42 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.82 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350, 0.2 M Li2SO4, 0.1 M bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.006 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 2.4→26.51 Å / Num. obs: 16005 / % possible obs: 99.2 % / Redundancy: 9.756 % / Biso Wilson estimate: 81.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.118 / Χ2: 1.388 / Net I/σ(I): 9.77 / Num. measured all: 156137
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.558.8145.9550.2921753252424680.26.29497.8
2.55-2.729.2732.7620.6421847239323560.2982.91798.5
2.72-2.949.8911.421.3121750221821990.6021.599.1
2.94-3.229.5180.5573.4319759208020760.9640.59199.8
3.22-3.610.3850.2169.6419535188618810.9910.22999.7
3.6-4.1510.1980.1416.6917113167916780.9940.14999.9
4.15-5.0810.4870.124.5215406146914690.9960.105100
5.08-7.1610.1650.07729.9911771115911580.9970.08199.9
7.16-26.5110.0040.04937.9172037207200.9990.052100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CN5

4cn5


Resolution: 2.4→26.51 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.957 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.397 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.486 / SU Rfree Blow DPI: 0.238 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.207 543 4.45 %RANDOM
Rwork0.191 ---
obs0.192 12203 75.6 %-
Displacement parametersBiso max: 197.39 Å2 / Biso mean: 83.26 Å2 / Biso min: 34.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.7256 Å20 Å20 Å2
2---1.7256 Å20 Å2
3---3.4512 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: final / Resolution: 2.4→26.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 855 11 36 2197
Biso mean--78.55 59.32 -
Num. residues----201
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d715SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes237HARMONIC5
X-RAY DIFFRACTIONt_it2278HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion286SEMIHARMONIC5
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_contact2255SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2278HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3224HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion22.96
LS refinement shellResolution: 2.4→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 37 4.52 %
Rwork0.215 781 -
all0.217 818 -
obs--21.86 %
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)
16.2718-0.7474-0.53266.2332-1.52626.7539-0.0762-0.228-0.17640.1690.1103-0.0161-0.20850.0196-0.0341-0.04130.152-0.0872-0.02240.0372-0.159114.1964-22.1246-17.5576
28.31550.6765-0.73626.26211.48295.6766-0.11480.1161-0.0425-0.1096-0.10890.54420.1654-0.26180.2237-0.15150.0085-0.0513-0.17460.03360.0924-8.3268-0.3352-31.2499
33.9483-2.14281.17836.0475-2.91044.7873-0.1607-0.54420.14280.5442-0.10220.3519-0.04830.48930.2629-0.18650.152-0.147-0.10430.0847-0.16543.0336-6.8335-11.1681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ C|132 - C|302 }C132 - 302
2X-RAY DIFFRACTION2{ D|82 - D|302 }D82 - 302
3X-RAY DIFFRACTION3{ A|1 - A|51 B|1 - B|21 }A1 - 51
4X-RAY DIFFRACTION3{ A|1 - A|51 B|1 - B|21 }B1 - 21

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