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- PDB-5q1h: Ligand binding to FARNESOID-X-RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 5q1h
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 / 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 ...regulation of urea metabolic process / 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 / 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 / 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 / positive regulation of female receptivity / bile acid binding / regulation of cholesterol metabolic process / cellular response to fatty acid / negative regulation of interleukin-2 production / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / hypothalamus development / bile acid and bile salt transport / male mating behavior / positive regulation of interleukin-17 production / intracellular glucose homeostasis / negative regulation of interleukin-6 production / negative regulation of type II interferon production / cellular response to Thyroglobulin triiodothyronine / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / Notch signaling pathway / : / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of neuron differentiation / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / hippocampus development / transcription coregulator binding / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / euchromatin / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development
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-9NP / 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 1.2Oct 4, 2017Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.3Dec 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 1.4Jan 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 1.5Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.6Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.identifier_ORCID / _citation.country / _citation_author.identifier_ORCID
Revision 1.7Nov 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 1.8Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
E: Bile acid receptor
F: COACTIVATOR PEPTIDE SRC-1 HD3
G: Bile acid receptor
H: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,49512
Polymers115,5618
Non-polymers1,9344
Water4,990277
1
A: Bile acid receptor
B: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3743
Polymers28,8902
Non-polymers4841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-6 kcal/mol
Surface area11990 Å2
MethodPISA
2
C: Bile acid receptor
D: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3743
Polymers28,8902
Non-polymers4841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9 kcal/mol
Surface area11870 Å2
MethodPISA
3
E: Bile acid receptor
F: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3743
Polymers28,8902
Non-polymers4841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-5 kcal/mol
Surface area11970 Å2
MethodPISA
4
G: Bile acid receptor
H: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3743
Polymers28,8902
Non-polymers4841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-5 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.414, 183.879, 55.787
Angle α, β, γ (deg.)90.000, 98.360, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4
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.: 4 / Fragment: UNP residues 744-757 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A8K1V4, UniProt: Q15788*PLUS
#3: Chemical
ChemComp-9NP / (2S)-N,2-dicyclohexyl-2-{2-[4-(1H-tetrazol-5-yl)phenyl]-1H-benzimidazol-1-yl}acetamide


Mass: 483.608 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H33N7O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 298 K / Method: evaporation, hanging drop / pH: 5.5 / Details: 0.1 M BIS-TRIS pH 5.5, 25%PEG3350

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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: Aug 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 55434 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.008 / Net I/σ(I): 15.6 / Num. measured all: 207659
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.283.10.66754911.25199.8
2.28-2.373.60.48855151.0161100
2.37-2.483.80.36155590.9231100
2.48-2.613.80.25455290.9651100
2.61-2.773.90.17155680.9491100
2.77-2.993.90.10755241.0051100
2.99-3.293.90.0755831.0121100
3.29-3.763.90.0555371.0181100
3.76-4.743.80.04355391.012199.9
4.741-353.70.03955890.993199.2

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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: 2.2→33.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.232 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.186
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2807 5.08 %RANDOM
Rwork0.18 ---
obs0.182 55294 99.1 %-
Displacement parametersBiso max: 148.22 Å2 / Biso mean: 59.17 Å2 / Biso min: 25.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.2885 Å20 Å2-0.2658 Å2
2--0.9997 Å20 Å2
3----1.2882 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.2→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7837 0 144 277 8258
Biso mean--45.99 60.38 -
Num. residues----956
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2972SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes229HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1138HARMONIC5
X-RAY DIFFRACTIONt_it8194HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1052SEMIHARMONIC5
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_contact9511SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8194HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11078HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion19.3
LS refinement shellResolution: 2.2→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2718 186 4.98 %
Rwork0.2237 3547 -
all0.226 3733 -
obs--91.35 %
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)
11.6637-0.42830.4623.8219-1.49762.452-0.1287-0.0633-0.01340.12550.21-0.0536-0.1419-0.1677-0.0813-0.2146-0.01510.0113-0.0513-0.0442-0.149133.45768.36334.1871
22.1006-0.2723-0.3672.14310.32143.8591-0.1233-0.19110.1095-0.13940.1347-0.0441-0.1660.3216-0.0114-0.0697-0.0403-0.0413-0.1559-0.0369-0.22644.087348.360418.8921
32.32641.03690.15244.07140.96332.1195-0.02050.2606-0.0753-0.0240.2552-0.2018-0.12530.104-0.2348-0.14480.00530.0284-0.06710.0177-0.19751.140820.497732.1821
43.04210.6337-0.14562.51570.77942.8527-0.007-0.1729-0.29070.12290.19190.06410.3040.1286-0.1849-0.18830.041-0.0611-0.15950.0471-0.104620.1606-19.84464.6162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A247 - 475
2X-RAY DIFFRACTION2{ C|* }C247 - 474
3X-RAY DIFFRACTION3{ E|* }E247 - 476
4X-RAY DIFFRACTION4{ G|* }G247 - 475

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