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- PDB-1pq6: HUMAN LXR BETA HORMONE RECEPTOR / GW3965 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1pq6
TitleHUMAN LXR BETA HORMONE RECEPTOR / GW3965 COMPLEX
ComponentsOxysterols receptor LXR-beta
Keywordstranscription regulation / LXRB+KB043546/WAY207380/GW3965
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 / regulation of lipid storage / positive regulation of triglyceride biosynthetic process / apolipoprotein A-I receptor binding / 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 / regulation of lipid storage / positive regulation of triglyceride biosynthetic process / apolipoprotein A-I receptor binding / 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 / positive regulation of fatty acid biosynthetic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / 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 / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of proteolysis / VLDLR internalisation and degradation / cholesterol homeostasis / response to nutrient levels / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / PPARA activates gene expression / chromatin DNA binding / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of gene expression / 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 / Double treble clef zinc finger, C4 type / 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 / Double treble clef zinc finger, C4 type / 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-965 / ISOPROPYL ALCOHOL / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFarnegardh, M. / Bonn, T. / Sun, S. / Ljunggren, J. / Ahola, H. / Wilhelmsson, A. / Gustafsson, J.-A. / Carlquist, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The three-dimensional structure of the liver X receptor beta reveals a flexible ligand-binding pocket that can accommodate fundamentally different ligands.
Authors: Farnegardh, M. / Bonn, T. / Sun, S. / Ljunggren, J. / Ahola, H. / Wilhelmsson, A. / Gustafsson, J.-A. / Carlquist, M.
History
DepositionJun 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)118,0959
Polymers116,2294
Non-polymers1,8665
Water3,009167
1
A: Oxysterols receptor LXR-beta
B: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3996
Polymers58,1152
Non-polymers1,2844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6973
Polymers58,1152
Non-polymers5821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-28 kcal/mol
Surface area21490 Å2
MethodPISA
3
A: Oxysterols receptor LXR-beta
hetero molecules

C: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3966
Polymers87,1723
Non-polymers1,2243
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Buried area6240 Å2
ΔGint-49 kcal/mol
Surface area31980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.717, 98.929, 175.815
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 orphan receptor LXR-beta / Ubiquitously-expressed nuclear receptor ...Liver X receptor beta / Nuclear orphan receptor LXR-beta / Ubiquitously-expressed nuclear receptor / Nuclear receptor NER


Mass: 29057.283 Da / Num. of mol.: 4 / Fragment: Ligand binding domain, residues 213-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H2 OR LXRB OR UNR OR NER / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: P55055
#2: Chemical ChemComp-965 / [3-(3-{[2-chloro-3-(trifluoromethyl)benzyl](2,2-diphenylethyl)amino}propoxy)phenyl]acetic acid


Mass: 582.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H31ClF3NO3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: isopropanol, PEG 4000, HEPES, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.5 %isopropanol1reservoir
217 %PEG40001reservoir
385 mMHEPES1reservoirpH7.5
415 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2002 / Details: Toroidal mirror
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.4→58 Å / Num. all: 40332 / Num. obs: 40332 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 46.99 Å2 / Rsym value: 0.045 / Net I/σ(I): 8.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 5585 / Rsym value: 0.218 / % possible all: 95.4
Reflection
*PLUS
Num. obs: 37733 / Num. measured all: 129438 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 95.4 % / Rmerge(I) obs: 0.218

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Thyroid hormone receptor beta

Resolution: 2.4→87.71 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.796 / SU ML: 0.208 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.511 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26237 2021 5 %RANDOM
Rwork0.20655 ---
all0.20934 40931 --
obs0.20934 38254 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.076 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2--1.03 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7375 0 131 167 7673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227652
X-RAY DIFFRACTIONr_bond_other_d0.0030.027154
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.97910342
X-RAY DIFFRACTIONr_angle_other_deg0.924316577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775898
X-RAY DIFFRACTIONr_chiral_restr0.0830.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028318
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021612
X-RAY DIFFRACTIONr_nbd_refined0.2030.21763
X-RAY DIFFRACTIONr_nbd_other0.2160.28183
X-RAY DIFFRACTIONr_nbtor_other0.0860.24673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2186
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.28
X-RAY DIFFRACTIONr_mcbond_it0.5341.54554
X-RAY DIFFRACTIONr_mcangle_it1.03927368
X-RAY DIFFRACTIONr_scbond_it1.74933098
X-RAY DIFFRACTIONr_scangle_it2.9974.52974
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 140
Rwork0.218 2689
Refinement
*PLUS
Highest resolution: 2.4 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.36
LS refinement shell
*PLUS
Highest resolution: 2.4 Å

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