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- PDB-1upv: Crystal structure of the human Liver X receptor beta ligand bindi... -

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Basic information

Entry
Database: PDB / ID: 1upv
TitleCrystal structure of the human Liver X receptor beta ligand binding domain in complex with a synthetic agonist
ComponentsOXYSTEROLS RECEPTOR LXR-BETA
KeywordsRECEPTOR / NUCLEAR HORMONE RECEPTOR / LIGAND BINDING DOMAIN / LIVER X RECEPTOR / TRANSCRIPTION FACTOR
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 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 / negative regulation of response to endoplasmic reticulum stress / negative regulation of pinocytosis / regulation of lipid storage / 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 / 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 / positive regulation of protein metabolic process / negative regulation of macrophage derived foam cell differentiation / positive regulation of cholesterol efflux / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / negative regulation of proteolysis / hormone-mediated signaling pathway / VLDLR internalisation and degradation / cholesterol homeostasis / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / PPARA activates gene expression / Nuclear Receptor transcription pathway / chromatin DNA binding / 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 / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHoerer, S. / Schmid, A. / Heckel, A. / Budzinski, R.M. / Nar, H.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of the Human Liver X Receptor Beta Ligand-Binding Domain in Complex with a Synthetic Agonist
Authors: Hoerer, S. / Schmid, A. / Heckel, A. / Budzinski, R.M. / Nar, H.
History
DepositionOct 13, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: OXYSTEROLS RECEPTOR LXR-BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8982
Polymers29,4171
Non-polymers4811
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)141.800, 43.200, 51.800
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein OXYSTEROLS RECEPTOR LXR-BETA / LIVER X RECEPTOR BETA / NUCLEAR ORPHAN / RECEPTOR LXR-BETA / UBIQUITOUSLY-EXPRESSED NUCLEAR ...LIVER X RECEPTOR BETA / NUCLEAR ORPHAN / RECEPTOR LXR-BETA / UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR / NUCLEAR RECEPTOR NER


Mass: 29416.621 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 209-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 1 / Source method: obtained synthetically / Formula: C17H12F9NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: ORPHAN RECEPTOR. BINDS PREFERENTIALLY TO DOUBLE-STRANDED OLIGONUCLEOTIDE DIRECT REPEATS ...FUNCTION: ORPHAN RECEPTOR. BINDS PREFERENTIALLY TO DOUBLE-STRANDED OLIGONUCLEOTIDE DIRECT REPEATS HAVING THE CONSENSUS HALF-SITE SEQUENCE 5'-AGGTCA-3' AND 4-NT SPACING (DR-4).

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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: 2.6 Å3/Da / Density % sol: 52.3 %
Crystal growpH: 7.5
Details: RESERVOIR: 25% MPD, 10% PEG4K, 100 MM HEPES PH 7.5, 10 MM D PROTEIN: 4-8 MG/ML IN 20 MM TRIS PH 8.0, 100 MM NACL, 10 MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9166
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9166 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 15111 / % possible obs: 83.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2 / % possible all: 71.3

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FCY

1fcy


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.541 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 755 5.1 %RANDOM
Rwork0.215 ---
obs-14163 83.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 16.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å22.34 Å2
2---2.27 Å20 Å2
3---2.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 31 97 2003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221945
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.982641
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7695230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021466
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.21009
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.521.51164
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05721880
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8893780
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3784.5761
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 54
Rwork0.234 902
Refinement TLS params.Method: refined / Origin x: 45.2994 Å / Origin y: -1.9624 Å / Origin z: 9.2113 Å
111213212223313233
T0.0526 Å2-0.0191 Å2-0.0441 Å2-0.0787 Å2-0.0129 Å2--0.0596 Å2
L1.5091 °2-0.3382 °2-1.0471 °2-1.152 °20.4559 °2--1.4883 °2
S0.0949 Å °-0.1107 Å °0.0775 Å °0.0294 Å °0.0299 Å °-0.1757 Å °-0.0977 Å °0.0926 Å °-0.1248 Å °

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