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- PDB-1uhl: Crystal structure of the LXRalfa-RXRbeta LBD heterodimer -

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Basic information

Entry
Database: PDB / ID: 1uhl
TitleCrystal structure of the LXRalfa-RXRbeta LBD heterodimer
Components
  • 10-mer peptide from Nuclear receptor coactivator 2
  • Oxysterols receptor LXR-alpha
  • Retinoic acid receptor RXR-beta
KeywordsDNA BINDING PROTEIN / ligand-binding domain
Function / homology
Function and homology information


negative regulation of secretion of lysosomal enzymes / sterol response element binding / negative 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 macrophage activation / negative regulation of pinocytosis / sterol homeostasis / positive regulation of toll-like receptor 4 signaling pathway ...negative regulation of secretion of lysosomal enzymes / sterol response element binding / negative 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 macrophage activation / negative regulation of pinocytosis / sterol homeostasis / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of lipoprotein lipase activity / positive regulation of triglyceride biosynthetic process / positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / positive regulation of fatty acid biosynthetic process / negative regulation of lipid transport / triglyceride homeostasis / anatomical structure development / positive regulation of vitamin D receptor signaling pathway / apoptotic cell clearance / negative regulation of cold-induced thermogenesis / cholesterol binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / lipid homeostasis / locomotor rhythm / aryl hydrocarbon receptor binding / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / positive regulation of lipid biosynthetic process / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / VLDLR internalisation and degradation / positive regulation of protein metabolic process / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / 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 receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of proteolysis / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / cellular response to lipopolysaccharide / transcription regulator complex / cell differentiation / transcription coactivator activity / protein dimerization activity / nuclear body / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding
Similarity search - Function
Liver X receptor / Retinoid X receptor/HNF4 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 ...Liver X receptor / Retinoid X receptor/HNF4 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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-444 / Chem-MEI / Retinoic acid receptor RXR-beta / Oxysterols receptor LXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSvensson, S. / Ostberg, T. / Jacobsson, M. / Norstrom, C. / Stefansson, K. / Hallen, D. / Johansson, I.C. / Zachrisson, K. / Ogg, D. / Jendeberg, L.
CitationJournal: Embo J. / Year: 2003
Title: Crystal structure of the heterodimeric complex of LXRalpha and RXRbeta ligand-binding domains in a fully agonistic conformation
Authors: Svensson, S. / Ostberg, T. / Jacobsson, M. / Norstrom, C. / Stefansson, K. / Hallen, D. / Johansson, I.C. / Zachrisson, K. / Ogg, D. / Jendeberg, L.
History
DepositionJul 3, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-beta
B: Oxysterols receptor LXR-alpha
C: 10-mer peptide from Nuclear receptor coactivator 2
D: 10-mer peptide from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6196
Polymers56,8704
Non-polymers7502
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.634, 88.996, 90.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Retinoic acid receptor RXR-beta / Retinoid X receptor


Mass: 26224.244 Da / Num. of mol.: 1 / Fragment: residues 298-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P28702
#2: Protein Oxysterols receptor LXR-alpha / Liver X receptor alpha / Nuclear orphan receptor LXR-alpha


Mass: 28092.203 Da / Num. of mol.: 1 / Fragment: residues 206-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q13133

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide 10-mer peptide from Nuclear receptor coactivator 2 / NCoA-2 / Transcriptional intermediary factor 2


Mass: 1276.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized / References: UniProt: Q15596

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Non-polymers , 3 types, 14 molecules

#4: Chemical ChemComp-MEI / (2E,4E)-11-METHOXY-3,7,11-TRIMETHYLDODECA-2,4-DIENOIC ACID / METOPRENIC ACID


Mass: 268.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H28O3
#5: 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.: 1 / Source method: obtained synthetically / Formula: C17H12F9NO3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 305 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, PEG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 305K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.11 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.9→19.65 Å / Num. all: 12550 / Num. obs: 12550 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.093 / Net I/σ(I): 9.2
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.42 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DKF

1dkf


Resolution: 2.9→19.65 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.795 / SU B: 18.823 / SU ML: 0.369 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.537 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32649 638 5.1 %RANDOM
Rwork0.21872 ---
all0.22394 12550 --
obs0.2239 12550 99.9 %-
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: 32.838 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 50 12 3707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0213762
X-RAY DIFFRACTIONr_angle_refined_deg2.7761.9785082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6185445
X-RAY DIFFRACTIONr_chiral_restr0.1940.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022787
X-RAY DIFFRACTIONr_nbd_refined0.2980.22012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.25
X-RAY DIFFRACTIONr_mcbond_it1.0161.52259
X-RAY DIFFRACTIONr_mcangle_it1.9323644
X-RAY DIFFRACTIONr_scbond_it3.0831503
X-RAY DIFFRACTIONr_scangle_it5.0854.51438
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.559 49
Rwork0.263 839

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