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- PDB-6xwh: Crystal Structure of the Human RXR DNA-Binding Domain Homodimer B... -

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Basic information

Entry
Database: PDB / ID: 6xwh
TitleCrystal Structure of the Human RXR DNA-Binding Domain Homodimer Bound to the Human Hoxb13 DR0 Response Element
Components
  • Hoxb13 DR0 Response Element, 3'-5' strand
  • Hoxb13 DR0 Response Element, 5'-3' strand
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / Protein-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
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 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
Similarity search - Domain/homology
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. / 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: Hoxb13 DR0 Response Element, 5'-3' strand
B: Hoxb13 DR0 Response Element, 3'-5' strand
C: Retinoic acid receptor RXR-alpha
D: Retinoic acid receptor RXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5858
Polymers30,3234
Non-polymers2624
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-29 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.705, 62.522, 53.635
Angle α, β, γ (deg.)90.000, 104.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain Hoxb13 DR0 Response Element, 5'-3' strand


Mass: 4981.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain Hoxb13 DR0 Response Element, 3'-5' strand


Mass: 4816.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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.: 2
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.15 M di-sodium DL-malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.1→22.22 Å / Num. obs: 15542 / % possible obs: 90.5 % / Redundancy: 3.008 % / Biso Wilson estimate: 71.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.056 / Χ2: 1.154 / Net I/σ(I): 9.21 / Num. measured all: 46744
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
2.1-2.232.05311.0820.0633502755163214.11259.2
2.23-2.382.3682.4610.335048257521323.07482.80.274
2.38-2.572.9921.3160.717313245024441.59599.80.535
2.57-2.823.4120.5591.877551221622130.66399.90.884
2.82-3.153.3850.1755.456803201620100.20999.70.989
3.15-3.633.3330.05414.995890177717670.06599.40.998
3.63-4.443.2840.03725.454945151815060.04599.20.999
4.44-6.263.2480.03231.643800118811700.03898.50.998
6.26-22.223.060.02835.4420446806680.03498.20.997

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.92 Å51.83 Å
Translation3.92 Å51.83 Å

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Processing

Software
NameVersionClassificationNB
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.5.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CN5

4cn5


Resolution: 2.1→22.22 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.361 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.224 548 4.92 %RANDOM
Rwork0.185 ---
obs0.187 11133 64.9 %-
Displacement parametersBiso max: 172.83 Å2 / Biso mean: 72.84 Å2 / Biso min: 34.63 Å2
Baniso -1Baniso -2Baniso -3
1--3.0277 Å20 Å2-1.4899 Å2
2--10.2189 Å20 Å2
3----7.1912 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: final / Resolution: 2.1→22.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 650 4 45 1981
Biso mean--69.7 58.38 -
Num. residues----190
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d671SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes227HARMONIC5
X-RAY DIFFRACTIONt_it2033HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion256SEMIHARMONIC5
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_contact2042SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2033HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2849HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion23
LS refinement shellResolution: 2.1→2.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.241 18 6.92 %
Rwork0.23 242 -
all0.231 260 -
obs--6.37 %
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)
18.9286-2.6815-1.07584.49870.52137.7023-0.2050.38670.1279-0.14240.3496-0.28480.4530.6655-0.1446-0.27740.018-0.0560.17860.0488-0.260224.3555-12.98663.8667
24.7291-0.25052.14465.7762-1.27897.9723-0.1681-0.51430.45790.3021-0.00710.3025-0.479-0.1840.1751-0.1301-0.0033-0.0741-0.1193-0.0646-0.08334.0045-5.7234-23.9572
30.4653-0.48160.83041.27730.70719.30660.0802-0.34150.05380.02020.0670.01340.6465-0.1704-0.1471-0.1791-0.0795-0.03140.17180.0229-0.176712.6085-13.5597-7.3978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ C|131 - C|302 }C131 - 302
2X-RAY DIFFRACTION2{ D|132 - D|302 }D132 - 302
3X-RAY DIFFRACTION3{ A|1 - A|16 B|1 - B|16 }A1 - 16
4X-RAY DIFFRACTION3{ A|1 - A|16 B|1 - B|16 }B1 - 16

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