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- PDB-6s4t: LXRbeta ligand binding domain in comlpex with small molecule inhi... -

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Basic information

Entry
Database: PDB / ID: 6s4t
TitleLXRbeta ligand binding domain in comlpex with small molecule inhibitors
ComponentsOxysterols receptor LXR-beta
KeywordsNUCLEAR PROTEIN / liver X receptor beta LXRb LXR beta Nuclear hormone receptor receptor ligand binding domain
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-KVB / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSandmark, J. / Jansson, A.
CitationJournal: Commun Biol / Year: 2019
Title: Structural analysis identifies an escape route from the adverse lipogenic effects of liver X receptor ligands.
Authors: Belorusova, A.Y. / Evertsson, E. / Hovdal, D. / Sandmark, J. / Bratt, E. / Maxvall, I. / Schulman, I.G. / Akerblad, P. / Lindstedt, E.L.
History
DepositionJun 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3273
Polymers28,2711
Non-polymers1,0552
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.275, 135.275, 69.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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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: 28271.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H2, LXRB, NER, UNR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55055
#2: Chemical ChemComp-KVB / 2-[4-[[3-[3-(phenylmethyl)-8-(trifluoromethyl)quinolin-4-yl]phenoxy]methyl]phenyl]ethanoic acid


Mass: 527.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H24F3NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 100 mM Bis-Tris pH 6.5, 2 M sodium formate and 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→95.8 Å / Num. obs: 22128 / % possible obs: 99.8 % / Redundancy: 9.2 % / Net I/σ(I): 5.5
Reflection shellResolution: 2→2.11 Å / Num. unique obs: 3155

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Processing

Software
NameVersionClassification
REFMAC5.8.0135 2015/10/01refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→62.017 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.329 / SU ML: 0.119 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.155
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2381 1132 -
Rwork0.2048 --
all0.207 --
obs-22054 99.702 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.909 Å2
Baniso -1Baniso -2Baniso -3
1--0.104 Å20 Å2-0 Å2
2---0.104 Å20 Å2
3---0.209 Å2
Refinement stepCycle: LAST / Resolution: 2→62.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 78 114 2125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192056
X-RAY DIFFRACTIONr_bond_other_d0.0060.021934
X-RAY DIFFRACTIONr_angle_refined_deg1.3212.0152787
X-RAY DIFFRACTIONr_angle_other_deg0.96834428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0365236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74823.63699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79815356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7581519
X-RAY DIFFRACTIONr_chiral_restr0.0740.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212309
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02470
X-RAY DIFFRACTIONr_nbd_refined0.2850.21002
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1550.23600
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21986
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.238
X-RAY DIFFRACTIONr_nbd_other0.1960.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.29
X-RAY DIFFRACTIONr_mcbond_it1.7573.682950
X-RAY DIFFRACTIONr_mcbond_other1.7573.679949
X-RAY DIFFRACTIONr_mcangle_it2.8695.5031184
X-RAY DIFFRACTIONr_mcangle_other2.8675.5071185
X-RAY DIFFRACTIONr_scbond_it1.9673.9861106
X-RAY DIFFRACTIONr_scbond_other2.0074.0751020
X-RAY DIFFRACTIONr_scangle_it3.3585.8671603
X-RAY DIFFRACTIONr_scangle_other3.4365.991481
X-RAY DIFFRACTIONr_lrange_it5.47829.132377
X-RAY DIFFRACTIONr_lrange_other5.56928.8532195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2-2.0520.306930.256150716001000.236
2.052-2.1080.298720.241148215541000.217
2.108-2.1690.301870.236145115381000.209
2.169-2.2360.248770.209139514721000.183
2.236-2.3090.251840.221136814521000.192
2.309-2.390.275770.217130513821000.186
2.39-2.480.25870.21127413611000.18
2.48-2.5810.261640.213123212961000.182
2.581-2.6960.24600.208117812381000.181
2.696-2.8270.248560.213115112071000.193
2.827-2.980.242550.21107811331000.194
2.98-3.160.329560.222102710831000.21
3.16-3.3780.264460.23697810241000.233
3.378-3.6470.248360.1939259611000.198
3.647-3.9940.183340.1728438771000.188
3.994-4.4630.18480.15675480399.87550.181
4.463-5.1490.17340.16668572099.86110.197
5.149-6.2960.214280.2195906181000.261
6.296-8.8580.236260.19845949597.97980.235
8.858-62.0170.206120.2824030482.89470.406

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