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- PDB-4j5x: Crystal Structure of the SR12813-bound PXR/RXRalpha LBD Heterotet... -

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Basic information

Entry
Database: PDB / ID: 4j5x
TitleCrystal Structure of the SR12813-bound PXR/RXRalpha LBD Heterotetramer Complex
Components
  • Nuclear receptor subfamily 1 group I member 2, Nuclear receptor coactivator 1
  • Retinoic acid receptor RXR-alpha, Nuclear receptor coactivator 1
KeywordsRetinoic acid-binding protein / Pregnane X Receptor / Retinoid X Receptor alpha / Ligand binding domain / nuclear receptor / SR12813 / alpha helical sandwich / unique intermolecular beta-sheet dimerization / xenobiotic sensing / upregulation of drug metabolism enzymes
Function / homology
Function and homology information


cellular response to molecule of bacterial origin / positive regulation of transporter activity / 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 / positive regulation of thyroid hormone receptor signaling pathway / intestinal epithelial structure maintenance / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle ...cellular response to molecule of bacterial origin / positive regulation of transporter activity / 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 / positive regulation of thyroid hormone receptor signaling pathway / intestinal epithelial structure maintenance / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / intermediate filament cytoskeleton / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / TGFBR3 expression / positive regulation of female receptivity / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / xenobiotic transport / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear steroid receptor activity / hypothalamus development / male mating behavior / LBD domain binding / steroid metabolic process / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / 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 / nuclear retinoid X receptor binding / xenobiotic catabolic process / response to retinoic acid / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / estrogen receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / : / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / xenobiotic metabolic process / positive regulation of neuron differentiation / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / peptide binding / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / hippocampus development / transcription coregulator binding / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / nuclear receptor activity / male gonad development / sequence-specific double-stranded DNA binding
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / : / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-SRL / Nuclear receptor subfamily 1 group I member 2 / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWallace, B.D. / Betts, L. / Redinbo, M.R.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural and Functional Analysis of the Human Nuclear Xenobiotic Receptor PXR in Complex with RXRalpha.
Authors: Wallace, B.D. / Betts, L. / Talmage, G. / Pollet, R.M. / Holman, N.S. / Redinbo, M.R.
History
DepositionFeb 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Retinoic acid receptor RXR-alpha, Nuclear receptor coactivator 1
C: Retinoic acid receptor RXR-alpha, Nuclear receptor coactivator 1
A: Nuclear receptor subfamily 1 group I member 2, Nuclear receptor coactivator 1
B: Nuclear receptor subfamily 1 group I member 2, Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0826
Polymers135,0734
Non-polymers1,0092
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-51 kcal/mol
Surface area46680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.090, 120.300, 175.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Retinoic acid receptor RXR-alpha, Nuclear receptor coactivator 1 / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha / NCoA-1 / Class E basic ...Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 29412.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR2B1, RXRA, BHLHE74, NCOA1, SRC1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI (DE3)
References: UniProt: P19793, UniProt: Q15788, histone acetyltransferase
#2: Protein Nuclear receptor subfamily 1 group I member 2, Nuclear receptor coactivator 1 / Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and ...Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and xenobiotic receptor / SXR / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 38123.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR, BHLHE74, NCOA1, SRC1 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI (DE3)
References: UniProt: O75469, UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-SRL / [2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC ACID DIETHLYL ESTER / SR12813


Mass: 504.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H42O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16-20% PEG 8000, 0.1-0.2 M MgCl, 0.1 M bis-tris proprane, 0.02% sodium azide, pH 7.0, vapor diffusion, hanging drop, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2012
RadiationMonochromator: Double crystal with K-B biomorph mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.735→99.279 Å / Num. obs: 40105 / Biso Wilson estimate: 37.44 Å2

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1037refinement
PDB_EXTRACT3.11data extraction
JBluIce-EPICSdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.646 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 1.99 / Phase error: 31.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2977 1830 4.93 %random
Rwork0.2452 ---
obs0.2479 37133 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.72 Å2 / Biso mean: 54.3479 Å2 / Biso min: 13.57 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8545 0 66 160 8771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048785
X-RAY DIFFRACTIONf_angle_d0.96611853
X-RAY DIFFRACTIONf_chiral_restr0.061319
X-RAY DIFFRACTIONf_plane_restr0.0041501
X-RAY DIFFRACTIONf_dihedral_angle_d20.1383388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.87570.37521510.31262607275898
2.8757-2.96030.35441450.300826792824100
2.9603-3.05580.38121440.275826782822100
3.0558-3.1650.34241340.268227042838100
3.165-3.29170.29571510.260826812832100
3.2917-3.44150.3051400.249127122852100
3.4415-3.62290.28391310.232627082839100
3.6229-3.84970.33451240.234427232847100
3.8497-4.14680.28941510.22862699285099
4.1468-4.56380.25791360.22522704284099
4.5638-5.22330.27111190.22152769288899
5.2233-6.57770.32371650.26382746291199
6.5777-45.65190.2261390.22242893303298

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