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- PDB-1pqc: HUMAN LXR BETA HORMONE RECEPTOR COMPLEXED WITH T0901317 -

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Basic information

Entry
Database: PDB / ID: 1pqc
TitleHUMAN LXR BETA HORMONE RECEPTOR COMPLEXED WITH T0901317
ComponentsOxysterols receptor LXR-beta
Keywordstranscription regulation / LXRB+T0901317
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 / cytoplasm / cytosol
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-444 / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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: 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)118,1548
Polymers116,2294
Non-polymers1,9254
Water3,261181
1
A: Oxysterols receptor LXR-beta
B: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0774
Polymers58,1152
Non-polymers9632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-17 kcal/mol
Surface area22350 Å2
MethodPISA
2
C: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0774
Polymers58,1152
Non-polymers9632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-16 kcal/mol
Surface area22010 Å2
MethodPISA
3
A: Oxysterols receptor LXR-beta
B: 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)118,1548
Polymers116,2294
Non-polymers1,9254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area8950 Å2
ΔGint-45 kcal/mol
Surface area42760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.722, 103.262, 176.002
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 213-261
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-444 / N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE


Mass: 481.333 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H12F9NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 12, 2002 / Details: mirrors
RadiationMonochromator: Osmic maxflux confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→40.49 Å / Num. all: 27198 / Num. obs: 27153 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 63.7 Å2 / Rsym value: 0.084 / Net I/σ(I): 7.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3882 / Rsym value: 0.402 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 92460 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.402

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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 ligand binding domain

Resolution: 2.8→40 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.892 / SU B: 15.914 / SU ML: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 1381 5.1 %RANDOM
Rwork0.19526 ---
all0.19861 27198 --
obs0.19861 25718 99.91 %-
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: 24.302 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--1.29 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7477 0 124 181 7782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227745
X-RAY DIFFRACTIONr_bond_other_d0.0020.027177
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9810502
X-RAY DIFFRACTIONr_angle_other_deg0.842316631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.21189
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028385
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021612
X-RAY DIFFRACTIONr_nbd_refined0.2150.21833
X-RAY DIFFRACTIONr_nbd_other0.2240.28222
X-RAY DIFFRACTIONr_nbtor_other0.0880.24710
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5811.54613
X-RAY DIFFRACTIONr_mcangle_it1.14527458
X-RAY DIFFRACTIONr_scbond_it1.65933132
X-RAY DIFFRACTIONr_scangle_it3.054.53044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 100
Rwork0.279 1831
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.195
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_deg1.49
LS refinement shell
*PLUS
Highest resolution: 2.8 Å

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