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- PDB-1pq9: HUMAN LXR BETA HORMONE RECEPTOR COMPLEXED WITH T0901317 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1pq9
TitleHUMAN LXR BETA HORMONE RECEPTOR COMPLEXED WITH T0901317 COMPLEX
ComponentsOxysterols receptor LXR-beta
Keywordstranscription regulation / LXRB+T0901317 SPLIT
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-44B / benzenesulfonic acid / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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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)118,22712
Polymers116,2294
Non-polymers1,9978
Water3,261181
1
A: Oxysterols receptor LXR-beta
B: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1136
Polymers58,1152
Non-polymers9994
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)59,1136
Polymers58,1152
Non-polymers9994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint3 kcal/mol
Surface area22070 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)118,22712
Polymers116,2294
Non-polymers1,9978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area9500 Å2
ΔGint-6 kcal/mol
Surface area42940 Å2
MethodPISA
4
A: Oxysterols receptor LXR-beta
hetero molecules

D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1136
Polymers58,1152
Non-polymers9994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area3600 Å2
ΔGint3 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.866, 103.606, 176.378
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: pet 28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: P55055
#2: Chemical
ChemComp-BNS / benzenesulfonic acid / Benzenesulfonic acid


Mass: 158.175 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O3S
#3: Chemical
ChemComp-44B / 1,1,1,3,3,3-HEXAFLUORO-2-{4-[(2,2,2-TRIFLUOROETHYL)AMINO]PHENYL}PROPAN-2-OL


Mass: 341.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H8F9NO
#4: Water ChemComp-HOH / water / 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: 2.31 Å3/Da / Density % sol: 46.82 %
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 22, 2002 / Details: toroidal mirrors
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: 2.1→55.84 Å / Num. all: 63700 / Num. obs: 63700 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 35.44 Å2 / Rsym value: 0.276 / Net I/σ(I): 5
Reflection shellResolution: 2.1→2.155 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 9212 / Rsym value: 0.066 / % possible all: 100
Reflection
*PLUS
Num. obs: 62281 / % possible obs: 99.8 % / Num. measured all: 231983 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Lowest resolution: 2.21 Å / % possible obs: 100 % / Rmerge(I) obs: 0.276

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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: 2.1→55.84 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.4 / SU ML: 0.145 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25441 3201 5 %RANDOM
Rwork0.21424 ---
all0.21626 63700 --
obs0.21626 60499 99.73 %-
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: 20.228 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2--0.32 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→55.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7474 0 124 181 7779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227738
X-RAY DIFFRACTIONr_bond_other_d0.0020.027179
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.97810478
X-RAY DIFFRACTIONr_angle_other_deg0.841316637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1265908
X-RAY DIFFRACTIONr_chiral_restr0.0830.21184
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028385
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021616
X-RAY DIFFRACTIONr_nbd_refined0.2170.21732
X-RAY DIFFRACTIONr_nbd_other0.2260.27946
X-RAY DIFFRACTIONr_nbtor_other0.0870.24602
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2204
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.210
X-RAY DIFFRACTIONr_mcbond_it0.751.54613
X-RAY DIFFRACTIONr_mcangle_it1.41827457
X-RAY DIFFRACTIONr_scbond_it2.09333125
X-RAY DIFFRACTIONr_scangle_it3.474.53021
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 231
Rwork0.253 4432
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.38
LS refinement shell
*PLUS
Highest resolution: 2.1 Å

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