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- PDB-6fbr: Crystal Structure of the Human Retinoid X Receptor DNA-Binding Do... -

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Basic information

Entry
Database: PDB / ID: 6fbr
TitleCrystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human MEp DR1 Response Element, pH 4.2
Components
  • DNA (5'-D(*CP*TP*GP*GP*GP*TP*CP*AP*AP*AP*GP*TP*TP*CP*AP*TP*C)-3')
  • DNA (5'-D(*GP*AP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*CP*CP*CP*AP*G)-3')
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / TRANSCRIPTION-DNA COMPLEX / 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 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
Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. ...Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / DNA / DNA (> 10) / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMcEwen, A.G. / Poussin-Courmontagne, P. / Osz, J. / Rochel, N.
Funding support France, 4items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BSV8-0024-01 France
Fondation ARCSFI20121205585 France
French National Research AgencyANR-10-INSB-05-01 France
French National Research AgencyANR-10-LABX-0030-INRT France
CitationJournal: Mol. Cell. Endocrinol. / Year: 2019
Title: Modulation of RXR-DNA complex assembly by DNA context.
Authors: Osz, J. / McEwen, A.G. / Wolf, J. / Poussin-Courmontagne, P. / Peluso-Iltis, C. / Chebaro, Y. / Kieffer, B. / Rochel, N.
History
DepositionDec 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 17, 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: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor RXR-alpha
C: DNA (5'-D(*CP*TP*GP*GP*GP*TP*CP*AP*AP*AP*GP*TP*TP*CP*AP*TP*C)-3')
D: DNA (5'-D(*GP*AP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*CP*CP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,52810
Polymers30,9404
Non-polymers5886
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-35 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.659, 55.659, 166.131
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-304-

PEG

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Components

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Protein , 1 types, 2 molecules AB

#1: 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19793

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*CP*TP*GP*GP*GP*TP*CP*AP*AP*AP*GP*TP*TP*CP*AP*TP*C)-3')


Mass: 5202.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*AP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*CP*CP*CP*AP*G)-3')


Mass: 5211.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 140 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 40% PEG 300, 0.1M sodium phosphate citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.2821 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2821 Å / Relative weight: 1
ReflectionResolution: 2→46.29 Å / Num. obs: 19015 / % possible obs: 90.2 % / Redundancy: 4.624 % / Biso Wilson estimate: 52.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.127 / Χ2: 1.224 / Net I/σ(I): 8.79 / Num. measured all: 87918
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.124.183.280.3919480.1523.73258.9
2.12-2.274.7041.930.827970.3782.16889
2.27-2.454.7351.0811.5528570.6421.21497.6
2.45-2.684.6790.6392.5126400.8530.71996.7
2.68-34.6760.3224.8424150.9620.36297.9
3-3.464.8910.09312.0921490.9980.10597.6
3.46-4.234.7060.05422.4518410.9990.0698
4.23-5.964.5030.04329.3514720.9980.04998.1
5.96-46.294.0640.03434.418960.9990.03996.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.2refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FBQ

6fbq


Resolution: 2.1→46.29 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.212 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.232 869 5 %RANDOM
Rwork0.178 ---
obs0.181 17378 95.5 %-
Displacement parametersBiso max: 158.57 Å2 / Biso mean: 58.52 Å2 / Biso min: 32.71 Å2
Baniso -1Baniso -2Baniso -3
1--5.7438 Å20 Å20 Å2
2---5.7438 Å20 Å2
3---11.4877 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.1→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 691 31 134 2140
Biso mean--76.28 57.03 -
Num. residues----193
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d698SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes27HARMONIC2
X-RAY DIFFRACTIONt_gen_planes235HARMONIC5
X-RAY DIFFRACTIONt_it2128HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion265SEMIHARMONIC5
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_contact2261SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2128HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2977HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion20.49
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.268 121 5 %
Rwork0.235 2297 -
all0.236 2418 -
obs--83.71 %
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)
15.1928-1.14210.28232.6856-0.51335.6509-0.0733-0.12990.2834-0.0120.12640.0826-0.4429-0.072-0.0531-0.0873-0.0427-0.0273-0.07130.0486-0.1494-23.189924.54219.9389
22.18981.0478-0.18234.8217-1.684.77610.0111-0.0186-0.19910.3368-0.0409-0.25180.0660.34770.0297-0.05010.0057-0.0081-0.0516-0.0079-0.1726-19.55346.615935.6569
30.78890.35650.94350.8066-2.35442.77430.04480.08580.0792-0.16930.16290.00050.118-0.3866-0.20770.0154-0.05630.00130.0446-0.0301-0.2027-29.583913.650721.0803
40.7337-0.16390.64381.0818-1.184.59510.07150.01690.04090.02760.03890.03480.337-0.2017-0.1104-0.0178-0.0524-0.01250.0351-0.0248-0.1736-28.477911.915421.635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A131 - 208
2X-RAY DIFFRACTION2{ B|* }B126 - 210
3X-RAY DIFFRACTION3{ C|* }C1 - 17
4X-RAY DIFFRACTION4{ D|* }D1 - 17

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