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- PDB-5q0i: Ligand binding to FARNESOID-X-RECEPTOR -

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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 urea metabolic process / nuclear receptor-mediated bile acid signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / : / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid ...regulation of urea metabolic process / nuclear receptor-mediated bile acid signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic 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 / positive regulation of fatty acid oxidation / regulation of bile acid biosynthetic process / : / regulation of insulin secretion involved in cellular response to glucose stimulus / : / toll-like receptor 9 signaling pathway / intracellular receptor signaling pathway / negative regulation of monocyte chemotactic protein-1 production / bile acid metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / lncRNA binding / bile acid binding / cell-cell junction assembly / response to muscle activity / bile acid signaling pathway / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / cellular response to fatty acid / negative regulation of interleukin-2 production / regulation of cholesterol metabolic process / temperature homeostasis / positive regulation of interleukin-17 production / intracellular glucose homeostasis / response to starvation / fatty acid oxidation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / response to dietary excess / transcription factor binding / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / Synthesis of bile acids and bile salts / fatty acid homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / energy homeostasis / nuclear retinoid X receptor binding / brown fat cell differentiation / positive regulation of insulin receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Recycling of bile acids and salts / Notch signaling pathway / positive regulation of gluconeogenesis / digestion / positive regulation of adipose tissue development / respiratory electron transport chain / mitochondrion organization / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / transcription coregulator binding / gluconeogenesis / cholesterol homeostasis / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / negative regulation of smooth muscle cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / chromatin DNA binding / mRNA processing / PML body / positive regulation of DNA-binding transcription factor activity / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / nuclear receptor activity / Circadian Clock / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / DNA-binding transcription factor binding / neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of neuron apoptotic process
Similarity search - Function
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / 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. ...Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / 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 / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: molecular replacement

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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|* }

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