[English] 日本語
Yorodumi
- PDB-5q0i: Ligand binding to FARNESOID-X-RECEPTOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5q0i
TitleLigand binding to FARNESOID-X-RECEPTOR
Components
  • Bile acid receptor
  • COACTIVATOR PEPTIDE PGC-1A PPAR GAMMA COACTIVATOR
KeywordsTRANSCRIPTION / D3R / FXR / Docking
Function / homology
Function and homology information


: / Regulation of MITF-M dependent genes involved in metabolism / : / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / : / positive regulation of ammonia assimilation cycle / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid ...: / Regulation of MITF-M dependent genes involved in metabolism / : / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / : / positive regulation of ammonia assimilation cycle / 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 / positive regulation of fatty acid oxidation / negative regulation of monocyte chemotactic protein-1 production / toll-like receptor 9 signaling pathway / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / cellular respiration / bile acid metabolic process / bile acid binding / cell-cell junction assembly / cellular response to fatty acid / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of cholesterol metabolic process / negative regulation of interleukin-2 production / response to starvation / bile acid and bile salt transport / response to muscle activity / temperature homeostasis / lncRNA binding / response to dietary excess / fatty acid oxidation / positive regulation of interleukin-17 production / intracellular glucose homeostasis / negative regulation of type II interferon production / negative regulation of interleukin-6 production / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor production / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / adipose tissue development / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of insulin secretion involved in cellular response to glucose stimulus / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Recycling of bile acids and salts / energy homeostasis / digestion / : / intracellular receptor signaling pathway / Notch signaling pathway / positive regulation of adipose tissue development / brown fat cell differentiation / positive regulation of gluconeogenesis / SUMOylation of transcription cofactors / RNA splicing / cholesterol homeostasis / negative regulation of canonical NF-kappaB signal transduction / nuclear receptor binding / transcription coregulator binding / gluconeogenesis / respiratory electron transport chain / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / mitochondrion organization / SUMOylation of intracellular receptors / transcription initiation at RNA polymerase II promoter / circadian regulation of gene expression / negative regulation of smooth muscle cell proliferation / Heme signaling / PPARA activates gene expression / euchromatin / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PML body / chromatin DNA binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / mRNA processing / Regulation of RUNX2 expression and activity / positive regulation of cold-induced thermogenesis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to oxidative stress / protein-containing complex assembly / neuron apoptotic process / sequence-specific DNA binding / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / transcription by RNA polymerase II
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Bile acid receptor, ligand binding domain / Thyroid hormone receptor / : / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...PGC-1alpha, RNA recognition motif / PGC-1 / Bile acid receptor, ligand binding domain / Thyroid hormone receptor / : / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding 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 / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-0X0 / cDNA FLJ52961, highly similar to Peroxisome proliferator-activated receptorgamma coactivator 1-alpha / Bile acid receptor / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
Model detailsStructures re-refined for D3R docking challenge
AuthorsRudolph, M.G. / Benz, J. / Burger, D. / Thoma, R. / Ruf, A. / Joseph, C. / Kuhn, B. / Shao, C. / Yang, H. / Burley, S.K.
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2018
Title: D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Authors: Gaieb, Z. / Liu, S. / Gathiaka, S. / Chiu, M. / Yang, H. / Shao, C. / Feher, V.A. / Walters, W.P. / Kuhn, B. / Rudolph, M.G. / Burley, S.K. / Gilson, M.K. / Amaro, R.E.
History
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.5Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.identifier_ORCID / _citation.country / _citation_author.identifier_ORCID
Revision 1.6Nov 17, 2021Group: Database references / Structure summary / Category: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
Revision 1.7May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bile acid receptor
B: COACTIVATOR PEPTIDE PGC-1A PPAR GAMMA COACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8283
Polymers28,3662
Non-polymers4631
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-10 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.648, 54.952, 108.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Bile acid receptor / Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H ...Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H member 4 / Retinoid X receptor-interacting protein 14 / RXR-interacting protein 14


Mass: 27100.191 Da / Num. of mol.: 1 / Fragment: UNP residues 258-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4, BAR, FXR, HRR1, RIP14 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RI1
#2: Protein/peptide COACTIVATOR PEPTIDE PGC-1A PPAR GAMMA COACTIVATOR


Mass: 1265.627 Da / Num. of mol.: 1 / Fragment: UNP residues 106-117 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: B7Z7E0, UniProt: Q9UBK2*PLUS
#3: Chemical ChemComp-0X0 / 2-[(3,4-dimethoxyphenyl)-(4-methylphenyl)sulfonyl-amino]-N-(2,4-dimethylpentan-3-yl)ethanamide


Mass: 462.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34N2O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.9 Å3/Da / Density % sol: 35.17 %
Crystal growTemperature: 298 K / Method: evaporation, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30.3 Å / Num. all: 24340 / Num. obs: 23081 / % possible obs: 94.8 % / Redundancy: 3.46 % / Rmerge(I) obs: 0.0737 / Net I/σ(I): 10.75
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 1.45 % / Rmerge(I) obs: 0.4387 / Num. possible: 3741 / Num. unique obs: 2825 / Net I/σ(I) obs: 1.75 / % possible all: 75.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
HKL-2000data scaling
PDB_EXTRACT3.23data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→18.66 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.136 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1171 5.09 %RANDOM
Rwork0.185 ---
obs0.187 23010 94.9 %-
Displacement parametersBiso max: 104.35 Å2 / Biso mean: 31.47 Å2 / Biso min: 12.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.5626 Å20 Å20 Å2
2--2.3143 Å20 Å2
3----4.8769 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.7→18.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 32 165 2139
Biso mean--34.16 42.74 -
Num. residues----239
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d812SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes315HARMONIC5
X-RAY DIFFRACTIONt_it2145HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion284SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2691SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2145HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2925HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion18.22
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2604 105 4.93 %
Rwork0.2426 2026 -
all0.2435 2131 -
obs--73.24 %
Refinement TLS params.Method: refined / Origin x: 35.1769 Å / Origin y: 29.4144 Å / Origin z: 39.7719 Å
111213212223313233
T-0.0007 Å20.0015 Å20.0083 Å2--0.0545 Å20.0129 Å2---0.0192 Å2
L0.8181 °2-0.0115 °2-0.0687 °2-0.5435 °2-0.3244 °2--0.6566 °2
S-0.0196 Å °0.1006 Å °0.0985 Å °-0.0335 Å °0.0314 Å °-0.0508 Å °0.0376 Å °-0.1038 Å °-0.0118 Å °
Refinement TLS groupSelection details: { A|* }

+
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