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- PDB-6jio: Human LXR-beta in complex with a ligand -

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Basic information

Entry
Database: PDB / ID: 6jio
TitleHuman LXR-beta in complex with a ligand
ComponentsOxysterols receptor LXR-beta
KeywordsDNA BINDING PROTEIN / Nuclear receptor
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 / 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 ...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 / 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 / positive regulation of cholesterol 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 / hormone-mediated signaling pathway / VLDLR internalisation and degradation / 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 / cytosol / cytoplasm
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 ...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-BQ3 / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, Z. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)81773636 China
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Identify liver X receptor beta modulator building blocks by developing a fluorescence polarization-based competition assay.
Authors: Zhang, Z. / Chen, H. / Chen, Z. / Ding, P. / Ju, Y. / Gu, Q. / Xu, J. / Zhou, H.
History
DepositionFeb 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Oxysterols receptor LXR-beta
C: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,1836
Polymers124,6864
Non-polymers4972
Water64936
1
A: Oxysterols receptor LXR-beta
C: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5913
Polymers62,3432
Non-polymers2481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-16 kcal/mol
Surface area21190 Å2
MethodPISA
2
B: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5913
Polymers62,3432
Non-polymers2481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-16 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.137, 106.888, 150.803
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
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: 31171.588 Da / Num. of mol.: 4 / Mutation: Q259A, R261G, D262S, R264S
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-BQ3 / tert-butyl 7-amino-3,4-dihydroisoquinoline-2(1H)-carboxylate


Mass: 248.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 281 K / Method: evaporation / Details: 22% PEG 3350, 0.1 M Tris HCl pH 8.5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50.14 Å / Num. obs: 34182 / % possible obs: 100 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.8
Reflection shellResolution: 2.6→2.72 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4104 / Rrim(I) all: 0.296

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HJP

5hjp


Resolution: 2.6→50.01 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.913 / SU B: 42.116 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R: 1.354 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28478 1696 5 %RANDOM
Rwork0.2624 ---
obs0.2635 32375 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.436 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å2-0 Å20 Å2
2--4.77 Å2-0 Å2
3----1.75 Å2
Refinement stepCycle: 1 / Resolution: 2.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7522 0 36 36 7594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197701
X-RAY DIFFRACTIONr_bond_other_d0.0020.027141
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.96710462
X-RAY DIFFRACTIONr_angle_other_deg0.932316438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1355958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0523.907343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.619151268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1241556
X-RAY DIFFRACTIONr_chiral_restr0.0540.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021559
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1455.4983868
X-RAY DIFFRACTIONr_mcbond_other1.1455.4973867
X-RAY DIFFRACTIONr_mcangle_it2.1478.2284814
X-RAY DIFFRACTIONr_mcangle_other2.1468.2284815
X-RAY DIFFRACTIONr_scbond_it0.735.5643833
X-RAY DIFFRACTIONr_scbond_other0.735.5673834
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4178.3625649
X-RAY DIFFRACTIONr_long_range_B_refined7.40465.478406
X-RAY DIFFRACTIONr_long_range_B_other7.40565.4538405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 121 -
Rwork0.388 2357 -
obs--100 %
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)
11.0719-0.74070.17890.6352-0.26620.2765-0.05850.1519-0.0970.2165-0.02860.0412-0.1950.07230.08710.29820.01640.00610.33480.0320.07223.4833-3.1665-31.1274
21-0.2418-1.00080.21380.45281.28790.08050.1064-0.13690.0964-0.0973-0.06380.0794-0.22480.01680.17080.0069-0.07690.38470.03120.079516.8553-38.8638-8.2653
30.08330.15790.18550.38150.34490.66180.09230.0256-0.05670.10220.1437-0.18420.1451-0.2169-0.2360.2945-0.0107-0.01380.39740.03640.1806-20.1902-18.5541-34.9598
40.5651-0.06920.01740.0316-0.00280.00180.0758-0.0919-0.0376-0.0378-0.0657-0.00320.0027-0.0147-0.01020.2233-0.0835-0.0330.46870.0020.0297-0.2272-60.8636-0.4015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A218 - 477
2X-RAY DIFFRACTION2B218 - 477
3X-RAY DIFFRACTION3C218 - 477
4X-RAY DIFFRACTION4D221 - 477

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