[English] 日本語
Yorodumi
- PDB-1osh: A Chemical, Genetic, and Structural Analysis of the nuclear bile ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1osh
TitleA Chemical, Genetic, and Structural Analysis of the nuclear bile acid receptor FXR
ComponentsBile acid receptor
KeywordsTRANSCRIPTION / Nuclear Receptor / Ligand Binding Domain
Function / homology
Function and homology information


regulation of urea metabolic process / intracellular bile acid receptor signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / bile acid receptor activity / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid ...regulation of urea metabolic process / intracellular bile acid receptor signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / bile acid receptor activity / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / regulation of bile acid biosynthetic process / regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to organonitrogen compound / toll-like receptor 9 signaling pathway / negative regulation of monocyte chemotactic protein-1 production / intracellular receptor signaling pathway / bile acid metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / bile acid binding / cell-cell junction assembly / bile acid signaling pathway / negative regulation of interleukin-2 production / cellular response to fatty acid / regulation of cholesterol metabolic process / positive regulation of interleukin-17 production / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor-mediated signaling pathway / fatty acid homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / negative regulation of canonical NF-kappaB signal transduction / positive regulation of insulin receptor signaling pathway / Recycling of bile acids and salts / Notch signaling pathway / positive regulation of adipose tissue development / cholesterol homeostasis / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / euchromatin / PPARA activates gene expression / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / nuclear receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm
Similarity search - Function
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / 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 ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / 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
Chem-FEX / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsDownes, M. / Verdecia, M.A. / Roecker, A.J. / Hughes, R. / Hogenesch, J.B. / Kast-Woelbern, H.R. / Bowman, M.E. / Ferrer, J.-L. / Anisfeld, A.M. / Edwards, P.A. ...Downes, M. / Verdecia, M.A. / Roecker, A.J. / Hughes, R. / Hogenesch, J.B. / Kast-Woelbern, H.R. / Bowman, M.E. / Ferrer, J.-L. / Anisfeld, A.M. / Edwards, P.A. / Rosenfeld, J.M. / Alvarez, J.G.A. / Noel, J.P. / Nicolaou, K.C. / Evans, R.M.
CitationJournal: Mol.Cell / Year: 2003
Title: A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR
Authors: Downes, M. / Verdecia, M.A. / Roecker, A.J. / Hughes, R. / Hogenesch, J.B. / Kast-Woelbern, H.R. / Bowman, M.E. / Ferrer, J.-L. / Anisfeld, A.M. / Edwards, P.A. / Rosenfeld, J.M. / Alvarez, ...Authors: Downes, M. / Verdecia, M.A. / Roecker, A.J. / Hughes, R. / Hogenesch, J.B. / Kast-Woelbern, H.R. / Bowman, M.E. / Ferrer, J.-L. / Anisfeld, A.M. / Edwards, P.A. / Rosenfeld, J.M. / Alvarez, J.G. / Noel, J.P. / Nicolaou, K.C. / Evans, R.M.
History
DepositionMar 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: Bile acid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5842
Polymers27,0851
Non-polymers4991
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.656, 56.776, 117.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Bile acid receptor / Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Retinoid X receptor-interacting protein ...Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Retinoid X receptor-interacting protein 14 / RXR-interacting protein 14


Mass: 27085.064 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4 / Plasmid: pHIS8-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q96RI1
#2: Chemical ChemComp-FEX / METHYL 3-{3-[(CYCLOHEXYLCARBONYL){[4'-(DIMETHYLAMINO)BIPHENYL-4-YL]METHYL}AMINO]PHENYL}ACRYLATE / FEXARAMINE / Fexaramine


Mass: 498.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H38N2O3 / Comment: agonist*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, MgCl, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMDMSO1drop
215 mg/mlprotein1drop
315-20 %(w/v)PEG80001reservoir
4100 mMHEPES-Na1reservoirpH7.5
50.2 M1reservoirMgCl2
61 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A
DetectorDetector: CCD / Date: Sep 1, 2002
RadiationMonochromator: MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.78→58.72 Å / Observed criterion σ(I): 2 / Biso Wilson estimate: 22 Å2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1374830.08 / Data cutoff high rms absF: 1374830.08 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1165 5.2 %RANDOM
Rwork0.215 ---
obs0.234 22591 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8813 Å2 / ksol: 0.367676 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.35 Å20 Å20 Å2
2---3.48 Å20 Å2
3----2.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 1.8→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 37 179 1984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d1.85
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 151 5.1 %
Rwork0.386 2834 -
obs--77.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4FEXARAMINE.PARAMFEXARAMINE.TOP
Refinement
*PLUS
Highest resolution: 1.78 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.85

+
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