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- PDB-5q0m: Ligand binding to FARNESOID-X-RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 5q0m
TitleLigand binding to FARNESOID-X-RECEPTOR
Components
  • Bile acid receptor
  • COACTIVATOR PEPTIDE SRC-1 HD3
KeywordsTRANSCRIPTION / D3R / FXR / Docking
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 insulin secretion involved in cellular response to glucose stimulus / regulation of bile acid biosynthetic process / cellular response to organonitrogen compound / toll-like receptor 9 signaling pathway / negative regulation of monocyte chemotactic protein-1 production / bile acid metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / intracellular receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / cell-cell junction assembly / positive regulation of female receptivity / regulation of cholesterol metabolic process / bile acid binding / bile acid signaling pathway / negative regulation of interleukin-2 production / cellular response to fatty acid / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of interleukin-17 production / positive regulation of insulin secretion involved in cellular response to glucose stimulus / intracellular glucose homeostasis / negative regulation of interleukin-6 production / estrous cycle / negative regulation of type II interferon production / cellular response to Thyroglobulin triiodothyronine / 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / positive regulation of insulin receptor signaling pathway / histone acetyltransferase activity / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / histone acetyltransferase / Notch signaling pathway / cellular response to hormone stimulus / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / cholesterol homeostasis / BMAL1:CLOCK,NPAS2 activates circadian gene expression / nuclear receptor coactivator activity / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear estrogen receptor binding / transcription coregulator binding / nuclear receptor binding / hippocampus development / euchromatin / mRNA transcription by RNA polymerase II / Heme signaling / SUMOylation of intracellular receptors / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / response to estradiol / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity
Similarity search - Function
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-9L1 / Nuclear receptor coactivator / Nuclear receptor coactivator 1 / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bile acid receptor
B: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4303
Polymers28,8902
Non-polymers5401
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-7 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.562, 93.562, 45.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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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
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 SRC-1 HD3


Mass: 1790.026 Da / Num. of mol.: 1 / Fragment: UNP residues 744-757 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A8K1V4, UniProt: Q15788*PLUS
#3: Chemical ChemComp-9L1 / 5-{[(3beta,5beta,14beta,17alpha)-3-hydroxy-24-oxocholan-24-yl]amino}benzene-1,3-dicarboxylic acid


Mass: 539.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H45NO6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 298 K / Method: evaporation, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.4 M Sodium Citrate

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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: Sep 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→46.8 Å / Num. all: 11768 / Num. obs: 11752 / % possible obs: 99.9 % / Redundancy: 4.14 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.61
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.5434 / Num. possible: 1462 / Num. unique obs: 1454 / Net I/σ(I) obs: 1.86 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.23data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→40.514 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 31.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 584 4.98 %
Rwork0.1831 11151 -
obs0.1869 11735 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.31 Å2 / Biso mean: 55.674 Å2 / Biso min: 17.56 Å2
Refinement stepCycle: final / Resolution: 2.2→40.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 39 39 1989
Biso mean--59.51 52.86 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092002
X-RAY DIFFRACTIONf_angle_d1.0242710
X-RAY DIFFRACTIONf_chiral_restr0.3307
X-RAY DIFFRACTIONf_plane_restr0.006340
X-RAY DIFFRACTIONf_dihedral_angle_d10.5461681
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.42140.41531540.275127622916
2.4214-2.77170.27271420.221527562898
2.7717-3.49180.26871520.199727802932
3.4918-40.52040.22661360.151428532989
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.7007-0.05410.33670.46140.17350.623-0.457-0.01670.10020.18350.1052-0.26310.02930.26740.00390.260.09660.03610.4633-0.01940.56674.206723.485312.4027
20.0135-0.1202-0.01790.54020.34170.3764-0.1837-0.2891.0001-0.0362-0.4173-1.3731-0.2351-0.4195-0.10220.6461-0.0461-0.03750.5180.00030.7798-2.108450.7497-0.7235
30.8556-0.32730.22140.39380.03262.97910.12980.13940.4208-0.8083-0.3936-0.89740.10670.1328-0.02010.2957-0.01910.11670.3058-0.02090.3584-1.07436.9654-5.3171
41.53640.35940.17052.3447-2.14392.01030.031-0.01610.067-0.37870.1896-0.2014-0.15360.23310.00070.3035-0.04120.02280.2995-0.04270.2588-5.499432.1929-2.4529
50.1359-0.45360.65042.1547-1.62970.9953-0.0883-0.21530.03950.10150.21380.5593-0.3186-0.62190.00090.38990.14350.0640.5202-0.05140.483-16.496243.96372.6182
62.0637-0.1719-0.01391.3282-1.17621.0646-0.16940.08780.07510.1128-0.00440.08730.9455-0.3788-0.00020.2434-0.08390.0240.2997-0.00050.1989-5.991325.19161.2138
72.7128-0.4501-0.42030.2622-0.57393.3979-0.3296-0.6028-0.515-0.18220.4115-0.2141.1146-0.0110.03690.44170.00450.11220.3469-0.01140.3719-4.312817.77617.1568
83.2047-1.5716-0.77732.7018-0.94461.0226-0.2578-0.4022-0.0532-0.32390.48130.87850.3876-1.14350.19030.2415-0.1129-0.01080.5146-0.01660.3939-16.101428.83872.9674
90.85220.65710.51192.028-1.13481.7681-0.36310.94530.1174-2.0076-0.2885-0.0186-0.49250.6059-0.16330.59520.0127-0.05870.3489-0.05380.2829-7.474239.1521-15.4387
104.0814-4.13053.21344.7752-2.34544.0507-1.20880.35070.061-0.9504-0.6012-1.76411.04230.6471-1.73770.7298-0.06480.47220.33560.01440.48536.49732.7678-13.7324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 247 through 265 )A247 - 265
2X-RAY DIFFRACTION2chain 'A' and (resid 266 through 283 )A266 - 283
3X-RAY DIFFRACTION3chain 'A' and (resid 284 through 316 )A284 - 316
4X-RAY DIFFRACTION4chain 'A' and (resid 317 through 342 )A317 - 342
5X-RAY DIFFRACTION5chain 'A' and (resid 343 through 379 )A343 - 379
6X-RAY DIFFRACTION6chain 'A' and (resid 380 through 404 )A380 - 404
7X-RAY DIFFRACTION7chain 'A' and (resid 405 through 426 )A405 - 426
8X-RAY DIFFRACTION8chain 'A' and (resid 427 through 456 )A427 - 456
9X-RAY DIFFRACTION9chain 'A' and (resid 457 through 474 )A457 - 474
10X-RAY DIFFRACTION10chain 'B' and (resid 746 through 755 )B746 - 755

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