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- PDB-4rak: Crystal structure of nuclear receptor subfamily 1, group h, membe... -

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Basic information

Entry
Database: PDB / ID: 4rak
TitleCrystal structure of nuclear receptor subfamily 1, group h, member 2 (lxrb) complexed with partial agonist
ComponentsOxysterols receptor LXR-beta
KeywordsTRANSCRIPTION/AGONIST / NHR / NR1H2 / LXR-B / LXRB / UNR / NER-I / RIP15 / NER / Ligand Binding Domain / Nuclear Hormone Receptor / RXR / TRANSCRIPTION-AGONIST 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 / 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-652 / 1,4-BUTANEDIOL / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsNanao, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Liver X Receptor (LXR) partial agonists: Biaryl pyrazoles and imidazoles displaying a preference for LXR beta.
Authors: Kick, E. / Martin, R. / Xie, Y. / Flatt, B. / Schweiger, E. / Wang, T.L. / Busch, B. / Nyman, M. / Gu, X.H. / Yan, G. / Wagner, B. / Nanao, M. / Nguyen, L. / Stout, T. / Plonowski, A. / ...Authors: Kick, E. / Martin, R. / Xie, Y. / Flatt, B. / Schweiger, E. / Wang, T.L. / Busch, B. / Nyman, M. / Gu, X.H. / Yan, G. / Wagner, B. / Nanao, M. / Nguyen, L. / Stout, T. / Plonowski, A. / Schulman, I. / Ostrowski, J. / Kirchgessner, T. / Wexler, R. / Mohan, R.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 28, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3747
Polymers61,0862
Non-polymers1,2885
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-20 kcal/mol
Surface area22050 Å2
MethodPISA
2
A: Oxysterols receptor LXR-beta
B: Oxysterols receptor LXR-beta
hetero molecules

A: Oxysterols receptor LXR-beta
B: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,74814
Polymers122,1714
Non-polymers2,57710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area12990 Å2
ΔGint-58 kcal/mol
Surface area40090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.820, 120.630, 176.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Oxysterols receptor LXR-beta / Liver X receptor beta / Nuclear receptor NER / Nuclear receptor subfamily 1 group H member 2 / ...Liver X receptor beta / Nuclear receptor NER / Nuclear receptor subfamily 1 group H member 2 / Ubiquitously-expressed nuclear receptor


Mass: 30542.854 Da / Num. of mol.: 2 / Fragment: UNP residues 213-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H2, LXRB, NER, UNR / References: UniProt: P55055
#2: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-652 / 2-{2-[2-(2-chlorophenyl)propan-2-yl]-1-[3'-(methylsulfonyl)biphenyl-4-yl]-1H-imidazol-4-yl}propan-2-ol


Mass: 509.059 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H29ClN2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.35 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 38284 / % possible obs: 87.2 % / Redundancy: 6.4 %

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→53.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.595 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27068 1920 5 %RANDOM
Rwork0.22949 ---
obs0.23159 36359 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.366 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.304 Å
Refinement stepCycle: LAST / Resolution: 2.04→53.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 88 183 4078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194015
X-RAY DIFFRACTIONr_bond_other_d0.0010.023940
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9935443
X-RAY DIFFRACTIONr_angle_other_deg2.62939013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1715474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.77423.6200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.44115715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3751539
X-RAY DIFFRACTIONr_chiral_restr0.1150.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214490
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02971
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8415.3551881
X-RAY DIFFRACTIONr_mcbond_other3.795.3521880
X-RAY DIFFRACTIONr_mcangle_it5.2567.9672348
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.2396.0842133
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 138 -
Rwork0.297 2665 -
obs--100 %

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