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- PDB-1osh: A Chemical, Genetic, and Structural Analysis of the nuclear bile ... -

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Basic information

Entry
Database: PDB / ID: 1osh
TitleA Chemical, Genetic, and Structural Analysis of the nuclear bile acid receptor FXR
ComponentsBile acid receptor
KeywordsTRANSCRIPTION / Nuclear Receptor / Ligand Binding Domain
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 / cell-cell junction assembly / bile acid binding / regulation of cholesterol metabolic process / cellular response to fatty acid / negative regulation of interleukin-2 production / bile acid and bile salt transport / positive regulation of interleukin-17 production / intracellular glucose homeostasis / negative regulation of interleukin-6 production / negative regulation of type II interferon production / intracellular receptor signaling pathway / 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 / nuclear retinoid X receptor binding / positive regulation of insulin receptor signaling pathway / Recycling of bile acids and salts / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / Notch signaling pathway / cholesterol homeostasis / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / euchromatin / PPARA activates gene expression / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / transcription cis-regulatory region binding / defense response to bacterium / nuclear speck / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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. ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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-FEX / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsDownes, M. / Verdecia, M.A. / Roecker, A.J. / Hughes, R. / Hogenesch, J.B. / Kast-Woelbern, H.R. / Bowman, M.E. / Ferrer, J.-L. / Anisfeld, A.M. / Edwards, P.A. ...Downes, M. / Verdecia, M.A. / Roecker, A.J. / Hughes, R. / Hogenesch, J.B. / Kast-Woelbern, H.R. / Bowman, M.E. / Ferrer, J.-L. / Anisfeld, A.M. / Edwards, P.A. / Rosenfeld, J.M. / Alvarez, J.G.A. / Noel, J.P. / Nicolaou, K.C. / Evans, R.M.
CitationJournal: Mol.Cell / Year: 2003
Title: A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR
Authors: Downes, M. / Verdecia, M.A. / Roecker, A.J. / Hughes, R. / Hogenesch, J.B. / Kast-Woelbern, H.R. / Bowman, M.E. / Ferrer, J.-L. / Anisfeld, A.M. / Edwards, P.A. / Rosenfeld, J.M. / Alvarez, ...Authors: Downes, M. / Verdecia, M.A. / Roecker, A.J. / Hughes, R. / Hogenesch, J.B. / Kast-Woelbern, H.R. / Bowman, M.E. / Ferrer, J.-L. / Anisfeld, A.M. / Edwards, P.A. / Rosenfeld, J.M. / Alvarez, J.G. / Noel, J.P. / Nicolaou, K.C. / Evans, R.M.
History
DepositionMar 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bile acid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5842
Polymers27,0851
Non-polymers4991
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.656, 56.776, 117.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Retinoid X receptor-interacting protein ...Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Retinoid X receptor-interacting protein 14 / RXR-interacting protein 14


Mass: 27085.064 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4 / Plasmid: pHIS8-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q96RI1
#2: Chemical ChemComp-FEX / METHYL 3-{3-[(CYCLOHEXYLCARBONYL){[4'-(DIMETHYLAMINO)BIPHENYL-4-YL]METHYL}AMINO]PHENYL}ACRYLATE / FEXARAMINE


Mass: 498.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H38N2O3 / Comment: agonist*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, MgCl, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMDMSO1drop
215 mg/mlprotein1drop
315-20 %(w/v)PEG80001reservoir
4100 mMHEPES-Na1reservoirpH7.5
50.2 M1reservoirMgCl2
61 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A
DetectorDetector: CCD / Date: Sep 1, 2002
RadiationMonochromator: MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.78→58.72 Å / Observed criterion σ(I): 2 / Biso Wilson estimate: 22 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1374830.08 / Data cutoff high rms absF: 1374830.08 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1165 5.2 %RANDOM
Rwork0.215 ---
obs0.234 22591 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8813 Å2 / ksol: 0.367676 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.35 Å20 Å20 Å2
2---3.48 Å20 Å2
3----2.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 1.8→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 37 179 1984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d1.85
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 151 5.1 %
Rwork0.386 2834 -
obs--77.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4FEXARAMINE.PARAMFEXARAMINE.TOP
Refinement
*PLUS
Highest resolution: 1.78 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.85

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