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- PDB-6s4u: LXRbeta ligand binding domain in comlpex with small molecule inhi... -

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Basic information

Entry
Database: PDB / ID: 6s4u
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 / 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 / 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 / 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-KVK / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 18, 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.name
Revision 1.2May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2566
Polymers84,8143
Non-polymers1,4423
Water32418
1
A: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7522
Polymers28,2711
Non-polymers4811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7522
Polymers28,2711
Non-polymers4811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7522
Polymers28,2711
Non-polymers4811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.086, 125.086, 137.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
22Chains A C
33Chains B C

NCS ensembles :
ID
1
2
3

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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.: 3
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-KVK / 6-[4-[[3-oxidanyl-1,1-bis(oxidanylidene)-5-phenyl-2-propan-2-yl-3~{H}-1,2-thiazol-4-yl]amino]butyl]pyridine-2-sulfonamide


Mass: 480.601 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N4O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Unknown.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.81→20 Å / Num. obs: 30616 / % possible obs: 99.8 % / Redundancy: 6.6 % / Net I/σ(I): 16.56
Reflection shellResolution: 2.81→2.9 Å / Num. unique obs: 5170

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Processing

Software
NameVersionClassification
REFMAC5.8.0135 2015/10/01refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: FREE R-VALUE / ESU R: 0.611 / ESU R Free: 0.342
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2798 761 -
Rwork0.2532 --
all0.254 --
obs-30612 99.801 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.109 Å2
Baniso -1Baniso -2Baniso -3
1-3.225 Å21.612 Å20 Å2
2--3.225 Å2-0 Å2
3----10.461 Å2
Refinement stepCycle: LAST / Resolution: 2.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5742 0 96 18 5856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195644
X-RAY DIFFRACTIONr_bond_other_d00.025341
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9857686
X-RAY DIFFRACTIONr_angle_other_deg4.095312159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0395696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33123.852244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.27415896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.541538
X-RAY DIFFRACTIONr_chiral_restr0.080.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216363
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021284
X-RAY DIFFRACTIONr_nbd_refined0.160.21968
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2330.27916
X-RAY DIFFRACTIONr_nbtor_refined0.1540.25112
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0990.25144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0680.252
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.29
X-RAY DIFFRACTIONr_nbd_other0.2360.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0060.22
X-RAY DIFFRACTIONr_mcbond_it3.8837.3712805
X-RAY DIFFRACTIONr_mcbond_other3.7837.3692804
X-RAY DIFFRACTIONr_mcangle_it4.32810.9713494
X-RAY DIFFRACTIONr_mcangle_other4.34310.9743495
X-RAY DIFFRACTIONr_scbond_it7.0977.9662839
X-RAY DIFFRACTIONr_scbond_other7.2247.9772738
X-RAY DIFFRACTIONr_scangle_it9.50411.6644192
X-RAY DIFFRACTIONr_scangle_other9.67111.6684043
X-RAY DIFFRACTIONr_lrange_it9.97558.2985728
X-RAY DIFFRACTIONr_lrange_other10.05957.9385622
X-RAY DIFFRACTIONr_ncsr_local_group_10.1220.0526002
X-RAY DIFFRACTIONr_ncsr_local_group_20.1210.0525696
X-RAY DIFFRACTIONr_ncsr_local_group_30.1160.0525426
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
2.81-2.8830.441490.3922144221698.96210.341
2.883-2.9620.375510.362214621971000.32
2.962-3.0470.382550.3382053210999.95260.299
3.047-3.140.373490.3232006205699.95140.284
3.14-3.2430.318500.324192619761000.292
3.243-3.3560.29460.3031886193399.94830.273
3.356-3.4820.299370.281181618531000.249
3.482-3.6230.248470.261175918061000.241
3.623-3.7830.247490.242168217311000.222
3.783-3.9670.238470.2471624167299.94020.219
3.967-4.180.208490.2221540159199.87430.207
4.18-4.4310.276470.2061456150499.93350.196
4.431-4.7340.273340.2131352139199.64050.208
4.734-5.1080.27450.2081270132099.62120.208
5.108-5.5890.236290.2591202123499.75690.256
5.589-6.2370.317360.2751077111499.91020.272
6.237-7.1790.207120.2839819931000.287
7.179-8.7390.178130.19983384999.64660.224
8.739-12.1390.25780.16766867999.55820.193
12.139-45.6850.6280.3224304381000.367

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