[English] 日本語
Yorodumi
- PDB-7axj: Crystal structure of the hPXR-LBD in complex with estradiol and c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7axj
TitleCrystal structure of the hPXR-LBD in complex with estradiol and clotrimazole
ComponentsNuclear receptor subfamily 1 group I member 2
KeywordsNUCLEAR PROTEIN / NUCLEAR RECEPTOR HORMONE RECEPTOR PREGNANE X RECEPTOR
Function / homology
Function and homology information


xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity ...xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm
Similarity search - Function
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. ...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
1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE / ESTRADIOL / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDelfosse, V. / Granell, M. / Blanc, P. / Bourguet, W.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-INBS-04-01 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-05 France
European Union (EU)825489 France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Mechanistic insights into the synergistic activation of the RXR-PXR heterodimer by endocrine disruptor mixtures.
Authors: Delfosse, V. / Huet, T. / Harrus, D. / Granell, M. / Bourguet, M. / Gardia-Parege, C. / Chiavarina, B. / Grimaldi, M. / Le Mevel, S. / Blanc, P. / Huang, D. / Gruszczyk, J. / Demeneix, B. / ...Authors: Delfosse, V. / Huet, T. / Harrus, D. / Granell, M. / Bourguet, M. / Gardia-Parege, C. / Chiavarina, B. / Grimaldi, M. / Le Mevel, S. / Blanc, P. / Huang, D. / Gruszczyk, J. / Demeneix, B. / Cianferani, S. / Fini, J.B. / Balaguer, P. / Bourguet, W.
History
DepositionNov 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear receptor subfamily 1 group I member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3653
Polymers36,7471
Non-polymers6172
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, A DIMERIC FORM REMAINS HYPOTHETICAL
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
2
A: Nuclear receptor subfamily 1 group I member 2
hetero molecules

A: Nuclear receptor subfamily 1 group I member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7296
Polymers73,4952
Non-polymers1,2344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area4340 Å2
ΔGint-37 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.280, 91.280, 86.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

-
Components

#1: Protein Nuclear receptor subfamily 1 group I member 2 / 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


Mass: 36747.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: pET11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75469
#2: Chemical ChemComp-CL6 / 1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE / CLOTRIMAZOLE / Clotrimazole


Mass: 344.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H17ClN2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antifungal*YM
#3: Chemical ChemComp-EST / ESTRADIOL / Estradiol


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 50 - 100 mM imidazole 8 - 14% isopropanol / PH range: 7.0 - 7.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.3→45.64 Å / Num. obs: 16757 / % possible obs: 99.8 % / Redundancy: 9.4 % / Biso Wilson estimate: 43.97 Å2 / Rrim(I) all: 0.068 / Net I/σ(I): 20.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1204 / Rrim(I) all: 0.649

-
Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ILG

1ilg


Resolution: 2.3→35.91 Å / SU ML: 0.2368 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.8219
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 837 5 %RANDOM
Rwork0.1954 15909 --
obs0.1968 16746 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 45 98 2285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00262270
X-RAY DIFFRACTIONf_angle_d0.613084
X-RAY DIFFRACTIONf_chiral_restr0.0367343
X-RAY DIFFRACTIONf_plane_restr0.0034416
X-RAY DIFFRACTIONf_dihedral_angle_d19.1668852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.26511360.22062592X-RAY DIFFRACTION99.96
2.44-2.630.28591370.2282607X-RAY DIFFRACTION99.89
2.63-2.90.28831370.2312598X-RAY DIFFRACTION99.85
2.9-3.320.27281400.21992655X-RAY DIFFRACTION99.89
3.32-4.180.23131410.18842669X-RAY DIFFRACTION100
4.18-35.910.16431460.17092788X-RAY DIFFRACTION99.22

+
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