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- PDB-5jy3: CRYSTAL STRUCTURE OF LXRbeta (NUCLEAR RECEPTOR SUBFAMILY 1, GROUP... -

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Basic information

Entry
Database: PDB / ID: 5jy3
TitleCRYSTAL STRUCTURE OF LXRbeta (NUCLEAR RECEPTOR SUBFAMILY 1, GROUP H, MEMBER 2) COMPLEXED WITH BMS-852927
ComponentsOxysterols receptor LXR-beta
KeywordsTRANSCRIPTION / NHR / NR1H2 / LXR-B / LXRB / UNR / NER-I / RIP15 / NER
Function / homology
Function and homology information


positive regulation of secretion of lysosomal enzymes / positive regulation of high-density lipoprotein particle assembly / positive regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / positive regulation of cholesterol transport / negative regulation of response to endoplasmic reticulum stress / negative regulation of pinocytosis / positive regulation of lipoprotein lipase activity / apolipoprotein A-I receptor binding / positive regulation of triglyceride biosynthetic process ...positive regulation of secretion of lysosomal enzymes / positive regulation of high-density lipoprotein particle assembly / positive regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / positive regulation of cholesterol transport / negative regulation of response to endoplasmic reticulum stress / negative regulation of pinocytosis / positive regulation of lipoprotein lipase activity / apolipoprotein A-I receptor binding / positive regulation of triglyceride biosynthetic process / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of lipid storage / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / positive regulation of fatty acid biosynthetic process / negative regulation of lipid transport / negative regulation of cold-induced thermogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / positive regulation of cholesterol efflux / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of protein metabolic process / VLDLR internalisation and degradation / hormone-mediated signaling pathway / cholesterol homeostasis / negative regulation of proteolysis / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / PPARA activates gene expression / chromatin DNA binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Liver X receptor / 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 ...Liver X receptor / 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-6OX / 1,4-BUTANEDIOL / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMuckelbauer, J.K.
CitationJournal: ACS Med Chem Lett / Year: 2016
Title: Discovery of Highly Potent Liver X Receptor beta Agonists.
Authors: Kick, E.K. / Busch, B.B. / Martin, R. / Stevens, W.C. / Bollu, V. / Xie, Y. / Boren, B.C. / Nyman, M.C. / Nanao, M.H. / Nguyen, L. / Plonowski, A. / Schulman, I.G. / Yan, G. / Zhang, H. / ...Authors: Kick, E.K. / Busch, B.B. / Martin, R. / Stevens, W.C. / Bollu, V. / Xie, Y. / Boren, B.C. / Nyman, M.C. / Nanao, M.H. / Nguyen, L. / Plonowski, A. / Schulman, I.G. / Yan, G. / Zhang, H. / Hou, X. / Valente, M.N. / Narayanan, R. / Behnia, K. / Rodrigues, A.D. / Brock, B. / Smalley, J. / Cantor, G.H. / Lupisella, J. / Sleph, P. / Grimm, D. / Ostrowski, J. / Wexler, R.R. / Kirchgessner, T. / Mohan, R.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxysterols receptor LXR-beta
B: Oxysterols receptor LXR-beta
C: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,79010
Polymers122,1714
Non-polymers2,6186
Water2,702150
1
A: Oxysterols receptor LXR-beta
B: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3955
Polymers61,0862
Non-polymers1,3093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-24 kcal/mol
Surface area21810 Å2
MethodPISA
2
C: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3955
Polymers61,0862
Non-polymers1,3093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-24 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.660, 120.350, 55.720
Angle α, β, γ (deg.)90.000, 107.490, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-607-

HOH

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Components

#1: Protein
Oxysterols receptor LXR-beta / Liver X receptor beta / Nuclear receptor NER / Nuclear receptor subfamily 1 group H member 2 / ...Liver X receptor beta / Nuclear receptor NER / Nuclear receptor subfamily 1 group H member 2 / Ubiquitously-expressed nuclear receptor


Mass: 30542.854 Da / Num. of mol.: 4 / Fragment: UNP residues 213-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H2, LXRB, NER, UNR / Production host: Escherichia coli (E. coli) / References: UniProt: P55055
#2: Chemical
ChemComp-6OX / 2-[2-[2-[2,6-bis(chloranyl)phenyl]propan-2-yl]-1-[2-fluoranyl-4-[3-fluoranyl-4-(hydroxymethyl)-5-methylsulfonyl-phenyl] phenyl]imidazol-4-yl]propan-2-ol / BMS-852927


Mass: 609.511 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H28Cl2F2N2O4S
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→99.01 Å / Num. obs: 56715 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 56.857 Å2 / Rmerge(I) obs: 0.182 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.4 Å / Rmerge(I) obs: 2.01 / Mean I/σ(I) obs: 1.15 / Num. unique all: 12200 / % possible all: 91.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→99.01 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.772 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.499 / ESU R Free: 0.29 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 3466 7.8 %RANDOM
Rwork0.2254 ---
obs0.2288 41043 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 102.46 Å2 / Biso mean: 50.431 Å2 / Biso min: 17.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å2-1.07 Å2
2--2.1 Å20 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 2.4→99.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7462 0 172 150 7784
Biso mean--53.93 46.45 -
Num. residues----916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0227813
X-RAY DIFFRACTIONr_angle_refined_deg2.4431.99510590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7615907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.13423.42383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.421151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6541576
X-RAY DIFFRACTIONr_chiral_restr0.1710.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025879
X-RAY DIFFRACTIONr_nbd_refined0.2680.23997
X-RAY DIFFRACTIONr_nbtor_refined0.320.25179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3740.2248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.25
X-RAY DIFFRACTIONr_mcbond_it1.3431.54797
X-RAY DIFFRACTIONr_mcangle_it2.13227442
X-RAY DIFFRACTIONr_scbond_it3.36333514
X-RAY DIFFRACTIONr_scangle_it5.1414.53146
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 257 -
Rwork0.295 2993 -
all-3250 -
obs--97.33 %

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