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- PDB-1p8d: X-Ray Crystal Structure of LXR Ligand Binding Domain with 24(S),2... -

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Basic information

Entry
Database: PDB / ID: 1p8d
TitleX-Ray Crystal Structure of LXR Ligand Binding Domain with 24(S),25-epoxycholesterol
Components
  • Oxysterols receptor LXR-beta
  • nuclear receptor coactivator 1 isoform 3
KeywordsMEMBRANE PROTEIN/PROTEIN BINDING / LXR / epoxycholesterol / nuclear receptor / steroid receptor / liver X receptor / transcription / MEMBRANE PROTEIN-PROTEIN BINDING COMPLEX
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 / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / negative regulation of cold-induced thermogenesis / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / estrous cycle / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / histone acetyltransferase activity / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / RORA activates gene expression / VLDLR internalisation and degradation / positive regulation of protein metabolic process / lactation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cerebellum development / cholesterol homeostasis / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of proteolysis / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / response to estradiol / HATs acetylate histones / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / cell differentiation / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
Liver X receptor / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator ...Liver X receptor / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-CO1 / : / Oxysterols receptor LXR-beta / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWilliams, S. / Bledsoe, R.K. / Collins, J.L. / Boggs, S. / Lambert, M.H. / Miller, A.B. / Moore, J. / McKee, D.D. / Moore, L. / Nichols, J. ...Williams, S. / Bledsoe, R.K. / Collins, J.L. / Boggs, S. / Lambert, M.H. / Miller, A.B. / Moore, J. / McKee, D.D. / Moore, L. / Nichols, J. / Parks, D. / Watson, M. / Wisely, B. / Willson, T.M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: X-ray crystal structure of the liver X receptor beta ligand binding domain: regulation by a histidine-tryptophan switch.
Authors: Williams, S. / Bledsoe, R.K. / Collins, J.L. / Boggs, S. / Lambert, M.H. / Miller, A.B. / Moore, J. / McKee, D.D. / Moore, L. / Nichols, J. / Parks, D. / Watson, M. / Wisely, B. / Willson, T.M.
History
DepositionMay 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 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: nuclear receptor coactivator 1 isoform 3
D: nuclear receptor coactivator 1 isoform 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8756
Polymers63,0744
Non-polymers8012
Water1,78399
1
A: Oxysterols receptor LXR-beta
C: nuclear receptor coactivator 1 isoform 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9383
Polymers31,5372
Non-polymers4011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-12 kcal/mol
Surface area12480 Å2
MethodPISA
2
B: Oxysterols receptor LXR-beta
D: nuclear receptor coactivator 1 isoform 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9383
Polymers31,5372
Non-polymers4011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-11 kcal/mol
Surface area12530 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-33 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.166, 120.012, 147.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-33-

HOH

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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: 28730.887 Da / Num. of mol.: 2
Fragment: Liver X Receptor beta ligand binding domain (residues 214-461)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H2 OR LXRB OR UNR OR NER / Plasmid: pHTC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: P55055
#2: Protein/peptide nuclear receptor coactivator 1 isoform 3 / Steroid Receptor Co-activator 1 / SRC1


Mass: 2806.163 Da / Num. of mol.: 2
Fragment: Steroid Receptor Co-activator 1 (residues 676-700)
Source method: obtained synthetically / Details: Pepetide synthesis / References: GenBank: 22538459, UniProt: Q15788*PLUS
#3: Chemical ChemComp-CO1 / 17-[3-(3,3-DIMETHYL-OXIRANYL)-1-METHYL-PROPYL]-10,13-DIMETHYL-2,3,4,7,8,9,10,11,12,13,14,15,16,17-TETRADECAHYDRO-1H-CYC LOPENTA[A]PHENANTHREN-3-OL / 24,25(S)-EPOXYCHOLESTEROL


Mass: 400.637 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H44O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10-12% PEG3350-8000, 0.2M NaCl , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-12 %PEG3350-80001reservoir
20.2 M1reservoirNaCl
312-14 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2001 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 15890 / Num. obs: 15658 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / Num. unique all: 2227 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 19175 / % possible obs: 95.3 % / Num. measured all: 141128 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 81.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RXR LBD

Resolution: 2.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1124 -RANDOM
Rwork0.214 ---
all0.214 15890 --
obs0.214 15658 98.5 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4119 0 58 99 4276
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.015
Refinement
*PLUS
Highest resolution: 2.7 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.014

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