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- PDB-4j5w: Crystal Structure of the apo-PXR/RXRalpha LBD Heterotetramer Complex -

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Basic information

Entry
Database: PDB / ID: 4j5w
TitleCrystal Structure of the apo-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 / alpha helical sandwich / unique intermolecular beta-sheet dimerization / xenobiotic sensing / upregulation of drug metabolism enzymes
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 / xenobiotic transport ...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 / xenobiotic transport / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / labyrinthine layer morphogenesis / positive regulation of vitamin D receptor signaling pathway / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / nuclear vitamin D receptor binding / positive regulation of female receptivity / intermediate filament cytoskeleton / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / steroid metabolic process / cellular response to Thyroglobulin triiodothyronine / estrous cycle / 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 / xenobiotic catabolic process / nuclear retinoid X receptor binding / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / xenobiotic metabolic process / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / hippocampus development / nuclear estrogen receptor 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 / cerebral cortex development / 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 / male gonad development / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / HATs acetylate histones / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / cell differentiation / receptor complex / nuclear body / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin 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 / DUF1518 ...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 / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
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
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
C: Retinoic acid receptor RXR-alpha, Nuclear receptor coactivator 1
D: Retinoic acid receptor RXR-alpha, Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1226
Polymers135,0734
Non-polymers492
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-53 kcal/mol
Surface area46620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.260, 109.550, 169.880
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 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: BHLHE74, NCOA1, NR1I2, PXR, SRC1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI (DE3)
References: UniProt: O75469, UniProt: Q15788, histone acetyltransferase
#2: 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: BHLHE74, NCOA1, NR2B1, RXRA, SRC1 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI (DE3)
References: UniProt: P19793, UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
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: Feb 20, 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: 2.773→92.067 Å / Num. obs: 34037 / Biso Wilson estimate: 43.71 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1061refinement
PDB_EXTRACT3.11data extraction
JBluIce-EPICSdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.536 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 0.42 / σ(F): 1.99 / Phase error: 32.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2981 1565 4.93 %random
Rwork0.2503 ---
obs0.2526 31721 95.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.58 Å2 / Biso mean: 35.327 Å2 / Biso min: 7.76 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8381 0 2 175 8558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048593
X-RAY DIFFRACTIONf_angle_d0.8811580
X-RAY DIFFRACTIONf_chiral_restr0.0591295
X-RAY DIFFRACTIONf_plane_restr0.0041478
X-RAY DIFFRACTIONf_dihedral_angle_d15.6023267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.89050.34881500.30752415256587
2.8905-2.99380.39391230.30062543266692
2.9938-3.11370.3941220.29662723284595
3.1137-3.25540.31771270.28632723285096
3.2554-3.4270.34061600.2692741290197
3.427-3.64160.27711440.25252729287397
3.6416-3.92270.30411250.23632782290797
3.9227-4.31720.26321520.21462790294298
4.3172-4.94140.25151530.21922832298599
4.9414-6.22350.26031630.25992847301099
6.2235-48.54280.29641460.23263031317799

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