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- PDB-6k9g: Human LXR-beta in complex with an agonist -

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Basic information

Entry
Database: PDB / ID: 6k9g
TitleHuman LXR-beta in complex with an agonist
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 / 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 / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / VLDLR internalisation and degradation / positive regulation of protein metabolic process / 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 / 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 / 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-D3R / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, Z. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)81773636 China
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Discovery of new LXR beta agonists as glioblastoma inhibitors.
Authors: Chen, H. / Chen, Z. / Zhang, Z. / Li, Y. / Zhang, S. / Jiang, F. / Wei, J. / Ding, P. / Zhou, H. / Gu, Q. / Xu, J.
History
DepositionJun 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: 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)126,8818
Polymers124,6864
Non-polymers2,1954
Water905
1
A: Oxysterols receptor LXR-beta
C: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4404
Polymers62,3432
Non-polymers1,0972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-17 kcal/mol
Surface area20080 Å2
MethodPISA
2
B: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4404
Polymers62,3432
Non-polymers1,0972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-17 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.433, 103.739, 152.233
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-D3R / ~{tert}-butyl (2'~{R},3~{R})-2'-[3-[4-(hydroxymethyl)-3-methylsulfonyl-phenyl]phenyl]-2-oxidanylidene-spiro[1~{H}-indole-3,3'-pyrrolidine]-1'-carboxylate


Mass: 548.650 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H32N2O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 281 K / Method: evaporation / Details: 22% PEG 3350, 0.1M 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: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→50.01 Å / Num. obs: 26810 / % possible obs: 99.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 21.9
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4967

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JIO

6jio


Resolution: 2.8→50.01 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.898 / SU B: 38.703 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 1355 5.1 %RANDOM
Rwork0.2607 ---
obs0.26174 25413 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 78.856 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å20 Å2
2--4.95 Å2-0 Å2
3----2.89 Å2
Refinement stepCycle: 1 / Resolution: 2.8→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6782 0 156 5 6943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197078
X-RAY DIFFRACTIONr_bond_other_d0.0020.026496
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9739703
X-RAY DIFFRACTIONr_angle_other_deg0.938314742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0795919
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73222.446233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23115986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1211543
X-RAY DIFFRACTIONr_chiral_restr0.0510.21179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021487
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_it0.9896.9073715
X-RAY DIFFRACTIONr_mcbond_other0.9886.9063714
X-RAY DIFFRACTIONr_mcangle_it1.76910.3464621
X-RAY DIFFRACTIONr_mcangle_other1.76910.3474622
X-RAY DIFFRACTIONr_scbond_it0.7486.7953363
X-RAY DIFFRACTIONr_scbond_other0.7486.7953364
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3710.2185083
X-RAY DIFFRACTIONr_long_range_B_refined3.2684.097663
X-RAY DIFFRACTIONr_long_range_B_other3.2684.0937664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 107 -
Rwork0.34 1825 -
obs--99.59 %
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)
13.44840.53230.44090.905-0.37720.3170.12290.0834-0.0512-0.0952-0.05070.06910.10360.0846-0.07220.06950.0377-0.03030.2346-0.00760.0881-0.3204-7.15511.1709
21.93660.001-0.78962.2464-0.27881.20180.0462-0.1226-0.25320.19160.0003-0.1685-0.2670.2348-0.04650.0806-0.05290.02260.20990.04440.1071.8163-2.035843.9264
31.75231.0277-0.55952.3998-0.26450.5090.1846-0.2511-0.1005-0.0374-0.03960.0429-0.16290.2397-0.1450.0918-0.10230.020.294-0.04570.1125-18.638713.79639.0481
41.6486-1.3814-0.74824.8959-0.29370.9158-0.1439-0.0788-0.1674-0.27110.24060.22980.0564-0.1663-0.09680.104-0.00280.05860.1570.06210.0868-20.6358-18.10942.55
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A220 - 477
2X-RAY DIFFRACTION2B219 - 475
3X-RAY DIFFRACTION3C219 - 477
4X-RAY DIFFRACTION4D220 - 476

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