[English] 日本語
Yorodumi
- PDB-7rio: human PXR LBD bound to GSK003 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rio
Titlehuman PXR LBD bound to GSK003
ComponentsIsoform 1C of Nuclear receptor subfamily 1 group I member 2
KeywordsGENE REGULATION / nuclear receptor / helical sandwhich
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 / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / 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
Chem-5YX / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.48 Å
AuthorsWilliams, S.P. / Wisely, G.B. / Ward, P.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Overcoming the Pregnane X Receptor Liability: Rational Design to Eliminate PXR-Mediated CYP Induction.
Authors: Ramanjulu, J.M. / Williams, S.P. / Lakdawala, A.S. / DeMartino, M.P. / Lan, Y. / Marquis, R.W.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,7982
Polymers34,1881
Non-polymers6111
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.392, 91.392, 85.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-676-

HOH

-
Components

#1: Protein Isoform 1C of 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: 34187.562 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: pRSETa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75469
#2: Chemical ChemComp-5YX / N-[3-(2-tert-butyl-5-{2-[2-(methanesulfonyl)ethyl]pyrimidin-4-yl}-1,3-thiazol-4-yl)-2-fluorophenyl]-2,5-difluorobenzene-1-sulfonamide


Mass: 610.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25F3N4O4S3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.73 % / Mosaicity: 0.995 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 50mM Imidazole pH7.2, 12% 2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 16406 / % possible obs: 99.4 % / Redundancy: 12.3 % / Biso Wilson estimate: 40.91 Å2 / Rmerge(I) obs: 0.106 / Χ2: 1.163 / Net I/σ(I): 10.4 / Num. measured all: 202590
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.3-2.3810.10.60116000.9891100
2.38-2.4813.50.56416150.8491100
2.48-2.5914.40.43616100.8981100
2.59-2.7311.10.4116202.49199.9
2.73-2.914.50.2116221.0571100
2.9-3.1214.40.14816351.1021100
3.12-3.4412.60.11216391.179199.6
3.44-3.9390.09116091.263196.5
3.93-4.9512.50.0716741.092199.6
4.95-4011.40.0617820.957198.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.16 Å
Translation2.5 Å31.16 Å

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER1.3.3phasing
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1ILH

1ilh


Resolution: 2.48→31.16 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 956 7.33 %
Rwork0.207 12078 -
obs0.2118 13034 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.35 Å2 / Biso mean: 42.8404 Å2 / Biso min: 20.18 Å2
Refinement stepCycle: final / Resolution: 2.48→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 40 84 2208
Biso mean--54.95 46.68 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.48-2.610.34141560.245717141870100
2.61-2.770.40821040.27131605170992
2.77-2.990.30151450.225117111856100
2.99-3.290.30031310.233617551886100
3.29-3.760.29461350.21341697183297
3.76-4.740.25131400.17441721186197
4.74-31.160.21471450.19031875202099

+
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://pdbjlvh1.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