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- PDB-5q0q: Ligand binding to FARNESOID-X-RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 5q0q
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


: / 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 ...: / 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 / 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 / bile acid metabolic process / bile acid binding / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / cell-cell junction assembly / cellular response to fatty acid / positive regulation of female receptivity / regulation of cholesterol metabolic process / negative regulation of interleukin-2 production / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / acyltransferase activity / bile acid and bile salt transport / male mating behavior / hypothalamus development / intracellular glucose homeostasis / positive regulation of interleukin-17 production / negative regulation of type II interferon production / negative regulation of interleukin-6 production / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / negative regulation of tumor necrosis factor production / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / negative regulation of tumor necrosis factor-mediated signaling pathway / Endogenous sterols / positive regulation of insulin receptor signaling pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / fatty acid homeostasis / response to retinoic acid / positive regulation of insulin secretion involved in cellular response to glucose stimulus / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / estrogen receptor signaling pathway / Notch signaling pathway / lactation / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / negative regulation of canonical NF-kappaB signal transduction / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / response to progesterone / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling / euchromatin / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / : / response to estradiol / HATs acetylate histones / cellular response to lipopolysaccharide / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding
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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / : / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-9LD / 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: 2.6 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
Revision 1.7May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
C: Bile acid receptor
D: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8546
Polymers57,7804
Non-polymers1,0732
Water1,40578
1
A: Bile acid receptor
B: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4273
Polymers28,8902
Non-polymers5371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-5 kcal/mol
Surface area11520 Å2
MethodPISA
2
C: Bile acid receptor
D: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4273
Polymers28,8902
Non-polymers5371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.439, 131.892, 37.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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.: 2
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.: 2 / Fragment: UNP residues 744-757 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A8K1V4, UniProt: Q15788*PLUS
#3: Chemical ChemComp-9LD / ethyl 4-({2-phenyl-5-[(thiophen-2-yl)sulfonyl]-4,5,6,7-tetrahydro-2H-pyrazolo[4,3-c]pyridine-3-carbonyl}amino)benzoate


Mass: 536.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24N4O5S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: evaporation, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 2.0 M Ammonium Sulfate

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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: May 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→47.7 Å / Num. all: 16387 / Num. obs: 16123 / % possible obs: 98.4 % / Redundancy: 5.34 % / Rmerge(I) obs: 0.1615 / Net I/σ(I): 7.68
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.81 % / Rmerge(I) obs: 0.6396 / Num. possible: 1726 / Num. unique obs: 1520 / Net I/σ(I) obs: 1.26 / % possible all: 88.1

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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: 2.6→37.41 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.868 / SU R Cruickshank DPI: 2.411 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.382 / SU Rfree Cruickshank DPI: 0.381
RfactorNum. reflection% reflectionSelection details
Rfree0.295 809 5.03 %RANDOM
Rwork0.246 ---
obs0.248 16079 98.4 %-
Displacement parametersBiso max: 155.85 Å2 / Biso mean: 58.54 Å2 / Biso min: 14.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.1698 Å20 Å20 Å2
2---4.6447 Å20 Å2
3---4.8145 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 2.6→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 74 78 3950
Biso mean--42.07 43.47 -
Num. residues----465
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1429SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes547HARMONIC5
X-RAY DIFFRACTIONt_it3954HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion507SEMIHARMONIC5
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_contact4448SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3954HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5339HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion1.9
X-RAY DIFFRACTIONt_other_torsion21.75
LS refinement shellResolution: 2.6→2.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4337 117 4.41 %
Rwork0.4025 2535 -
all0.4038 2652 -
obs--92.04 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5437-0.3667-0.51722.59110.57041.4435-0.070.0404-0.21290.11990.042-0.12330.08150.20750.028-0.1510.00810.0348-0.12770.0019-0.1342-31.35256.153-11.3629
24.9489-0.30950.51892.04550.70092.97280.00070.0676-0.09390.1174-0.1687-0.00710.2301-0.32660.168-0.15040.0017-0.0195-0.1283-0.0363-0.1802-0.01826.002-7.1252
30.36880.34230.32340.07570.44270.2763-0.0036-0.0070.02130.02630.00770.031-0.0192-0.0146-0.0041-0.02670.0096-0.02020.024-0.0985-0.02171.044645.07211.3425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A247 - 474
2X-RAY DIFFRACTION2{ C|* }C247 - 474
3X-RAY DIFFRACTION3{ D|* }D744 - 755

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