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- PDB-2acl: Liver X-Receptor alpha Ligand Binding Domain with SB313987 -

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Basic information

Entry
Database: PDB / ID: 2acl
TitleLiver X-Receptor alpha Ligand Binding Domain with SB313987
Components
  • Oxysterols receptor LXR-alpha
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / nuclear hormone receptor ligand binding domain transcription factor three layered a-helix fold
Function / homology
Function and homology information


negative regulation of secretion of lysosomal enzymes / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / sterol response element binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / cellular lipid metabolic process / negative regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / positive regulation of cholesterol transport ...negative regulation of secretion of lysosomal enzymes / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / sterol response element binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / cellular lipid metabolic process / 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 / VLDLR internalisation and degradation / positive regulation of toll-like receptor 4 signaling pathway / 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 / positive regulation of thyroid hormone mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / positive regulation of fatty acid biosynthetic process / negative regulation of lipid transport / triglyceride homeostasis / Carnitine metabolism / anatomical structure development / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / apoptotic cell clearance / negative regulation of cold-induced thermogenesis / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / positive regulation of cholesterol efflux / 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 / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / Recycling of bile acids and salts / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / 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 / Activation of gene expression by SREBF (SREBP) / response to progesterone / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide 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 / chromatin DNA binding / negative regulation of inflammatory response / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / fatty acid biosynthetic process / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / cell differentiation / 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 / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin / protein-containing complex binding
Similarity search - Function
Liver X receptor / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / 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) ...Liver X receptor / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / 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-L05 / RETINOIC ACID / Retinoic acid receptor RXR-alpha / Oxysterols receptor LXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJaye, M.C. / Krawiec, J.A. / Campobasso, N. / Smallwood, A. / Qiu, C. / Lu, Q. / Kerrigan, J.J.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Discovery of substituted maleimides as liver x receptor agonists and determination of a ligand-bound crystal structure.
Authors: Jaye, M.C. / Krawiec, J.A. / Campobasso, N. / Smallwood, A. / Qiu, C. / Lu, Q. / Kerrigan, J.J. / De Los Frailes Alvaro, M. / Laffitte, B. / Liu, W.S. / Marino, J.P. / Meyer, C.R. / Nichols, ...Authors: Jaye, M.C. / Krawiec, J.A. / Campobasso, N. / Smallwood, A. / Qiu, C. / Lu, Q. / Kerrigan, J.J. / De Los Frailes Alvaro, M. / Laffitte, B. / Liu, W.S. / Marino, J.P. / Meyer, C.R. / Nichols, J.A. / Parks, D.J. / Perez, P. / Sarov-Blat, L. / Seepersaud, S.D. / Steplewski, K.M. / Thompson, S.K. / Wang, P. / Watson, M.A. / Webb, C.L. / Haigh, D. / Caravella, J.A. / Macphee, C.H. / Willson, T.M. / Collins, J.L.
History
DepositionJul 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
B: Oxysterols receptor LXR-alpha
C: Retinoic acid receptor RXR-alpha
D: Oxysterols receptor LXR-alpha
E: Retinoic acid receptor RXR-alpha
F: Oxysterols receptor LXR-alpha
G: Retinoic acid receptor RXR-alpha
H: Oxysterols receptor LXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,16816
Polymers219,4288
Non-polymers2,7398
Water64936
1
A: Retinoic acid receptor RXR-alpha
B: Oxysterols receptor LXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5424
Polymers54,8572
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-29 kcal/mol
Surface area21320 Å2
MethodPISA
2
C: Retinoic acid receptor RXR-alpha
D: Oxysterols receptor LXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5424
Polymers54,8572
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-27 kcal/mol
Surface area21520 Å2
MethodPISA
3
E: Retinoic acid receptor RXR-alpha
F: Oxysterols receptor LXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5424
Polymers54,8572
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-28 kcal/mol
Surface area21480 Å2
MethodPISA
4
G: Retinoic acid receptor RXR-alpha
H: Oxysterols receptor LXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5424
Polymers54,8572
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-27 kcal/mol
Surface area20820 Å2
MethodPISA
5
C: Retinoic acid receptor RXR-alpha
D: Oxysterols receptor LXR-alpha
G: Retinoic acid receptor RXR-alpha
H: Oxysterols receptor LXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0848
Polymers109,7144
Non-polymers1,3704
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-82 kcal/mol
Surface area37780 Å2
MethodPISA
6
A: Retinoic acid receptor RXR-alpha
B: Oxysterols receptor LXR-alpha
E: Retinoic acid receptor RXR-alpha
F: Oxysterols receptor LXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0848
Polymers109,7144
Non-polymers1,3704
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-82 kcal/mol
Surface area38490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.77, 81.95, 111.44
Angle α, β, γ (deg.)88.98, 75.20, 78.27
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 26667.857 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19793
#2: Protein
Oxysterols receptor LXR-alpha / Liver X receptor alpha / Nuclear orphan receptor LXR-alpha


Mass: 28189.248 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr1h3, Lxra / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z0Y9
#3: Chemical
ChemComp-REA / RETINOIC ACID / Retinoic acid


Mass: 300.435 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H28O2
#4: Chemical
ChemComp-L05 / 1-BENZYL-3-(4-METHOXYPHENYLAMINO)-4-PHENYLPYRROLE-2,5-DIONE


Mass: 384.427 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H20N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350, Ammonium Acetate, BisTris, Dtt, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 96909

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNXrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2307 -Random
Rwork0.21 ---
all0.22 46345 --
obs0.22 96909 95 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14618 0 204 36 14858

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