[English] 日本語
Yorodumi
- PDB-4j5w: Crystal Structure of the apo-PXR/RXRalpha LBD Heterotetramer Complex -

+
Open data


ID or keywords:

Loading...

-
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


cellular response to molecule of bacterial origin / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / 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 ...cellular response to molecule of bacterial origin / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / 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 / positive regulation of female receptivity / TGFBR3 expression / 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 / male mating behavior / hypothalamus development / LBD domain binding / steroid metabolic process / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / 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 / response to retinoic acid / positive regulation of bone mineralization / xenobiotic catabolic process / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / estrogen receptor signaling pathway / hormone-mediated signaling pathway / lactation / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / peptide binding / xenobiotic metabolic process / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / 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 / RNA polymerase II transcription regulator complex / male gonad development / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear receptor activity / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / : / response to estradiol / nervous system development / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / receptor complex / transcription cis-regulatory region binding / protein dimerization activity / nuclear body
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more