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- PDB-6k9m: Human LXR-beta in complex with an agonist -

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Basic information

Entry
Database: PDB / ID: 6k9m
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 / 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-D43 / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 novel liver X receptor inverse agonists as lipogenesis inhibitors.
Authors: Chen, Z. / Chen, H. / Zhang, Z. / Ding, P. / Yan, X. / Li, Y. / Zhang, S. / Gu, Q. / Zhou, H. / Xu, J.
History
DepositionJun 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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)126,0088
Polymers124,6864
Non-polymers1,3224
Water1086
1
A: Oxysterols receptor LXR-beta
C: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0044
Polymers62,3432
Non-polymers6612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-16 kcal/mol
Surface area20620 Å2
MethodPISA
2
B: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0044
Polymers62,3432
Non-polymers6612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-16 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.863, 105.356, 150.430
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-D43 / ~{tert}-butyl (2'~{S},3~{S})-2-oxidanylidene-2'-propan-2-yl-spiro[1~{H}-indole-3,3'-pyrrolidine]-1'-carboxylate


Mass: 330.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H26N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 22% PEG3350, 0.1 M Tris HCl, pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50.01 Å / Num. obs: 23587 / % possible obs: 97.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 23.12
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.723 / Num. unique obs: 4346 / % possible all: 98.6

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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: 2.9→50.01 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.872 / SU B: 44.731 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27963 1136 4.8 %RANDOM
Rwork0.24308 ---
obs0.24479 22416 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.612 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2--2.35 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: 1 / Resolution: 2.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7252 0 96 6 7354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197520
X-RAY DIFFRACTIONr_bond_other_d0.0070.026927
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.96310263
X-RAY DIFFRACTIONr_angle_other_deg0.983315851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5055955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18723.557298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.671151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.341549
X-RAY DIFFRACTIONr_chiral_restr0.060.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218552
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021536
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_it0.6574.5933859
X-RAY DIFFRACTIONr_mcbond_other0.6574.5923858
X-RAY DIFFRACTIONr_mcangle_it1.1966.8784801
X-RAY DIFFRACTIONr_mcangle_other1.1966.8794802
X-RAY DIFFRACTIONr_scbond_it0.4684.5813661
X-RAY DIFFRACTIONr_scbond_other0.4684.5813662
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8786.8925463
X-RAY DIFFRACTIONr_long_range_B_refined2.36356.0948511
X-RAY DIFFRACTIONr_long_range_B_other2.36356.0968512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.902→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 83 -
Rwork0.319 1526 -
obs--92.74 %
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)
12.6577-1.15760.0631.67140.03141.4619-0.00560.10520.02290.0989-0.0228-0.0872-0.09790.08520.02830.0947-0.02080.00930.15650.03050.03143.7697-3.3385-31.26
22.0338-0.7051-0.27012.04330.23441.24190.0712-0.11680.1272-0.14640.0015-0.098-0.0552-0.052-0.07260.0634-0.0385-0.0190.2042-0.01880.036116.8284-38.7561-8.3985
30.491-0.40540.0443.0281-0.04222.14180.02490.09460.02370.03340.104-0.05910.3194-0.2462-0.12880.1172-0.0786-0.03180.2324-0.00530.0197-19.7015-18.9822-35.0778
44.33570.03670.50840.6296-0.19451.22530.3082-0.1134-0.3984-0.0077-0.1738-0.00570.0737-0.033-0.13440.1166-0.0508-0.07360.12870.02170.0713-0.3959-59.85810.2444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A219 - 477
2X-RAY DIFFRACTION2B218 - 477
3X-RAY DIFFRACTION3C218 - 477
4X-RAY DIFFRACTION4D221 - 477

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