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- PDB-1rdt: Crystal Structure of a new rexinoid bound to the RXRalpha ligand ... -

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Basic information

Entry
Database: PDB / ID: 1rdt
TitleCrystal Structure of a new rexinoid bound to the RXRalpha ligand binding doamin in the RXRalpha/PPARgamma heterodimer
Components
  • (LxxLL motif coactivator) x 2
  • Peroxisome proliferator activated receptor gamma
  • Retinoic acid receptor RXR-alpha
KeywordsHORMONE/GROWTH FACTOR / Hormone / receptor / polymorphism / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


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 receptor signaling pathway / peptide lactyltransferase (CoA-dependent) activity / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / NFE2L2 regulating ER-stress associated genes / Carnitine metabolism ...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 receptor signaling pathway / peptide lactyltransferase (CoA-dependent) activity / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / NFE2L2 regulating ER-stress associated genes / Carnitine metabolism / peptide N-acetyltransferase activity / ion binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / labyrinthine layer morphogenesis / MRF binding / positive regulation of vitamin D receptor signaling pathway / regulation of thyroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / positive regulation of transcription from RNA polymerase II promoter by galactose / nuclear vitamin D receptor binding / MECP2 regulates transcription factors / positive regulation of female receptivity / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / negative regulation of extracellular matrix assembly / RUNX3 regulates NOTCH signaling / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / Regulation of FOXO transcriptional activity by acetylation / NOTCH4 Intracellular Domain Regulates Transcription / negative regulation of cardiac muscle hypertrophy in response to stress / Regulation of gene expression by Hypoxia-inducible Factor / arachidonic acid binding / Nuclear events mediated by NFE2L2 / positive regulation of low-density lipoprotein receptor activity / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / NFE2L2 regulating anti-oxidant/detoxification enzymes / Signaling by Retinoic Acid / DNA binding domain binding / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / nuclear steroid receptor activity / STAT family protein binding / embryonic digit morphogenesis / hypothalamus development / positive regulation of fatty acid metabolic process / male mating behavior / response to lipid / homeostatic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of SMAD protein signal transduction / protein acetylation / Notch-HLH transcription pathway / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / negative regulation of cholesterol storage / non-canonical NF-kappaB signal transduction / E-box binding / alpha-actinin binding / lipid homeostasis / Zygotic genome activation (ZGA) / negative regulation of vascular associated smooth muscle cell proliferation / stimulatory C-type lectin receptor signaling pathway / R-SMAD binding / cellular response to nutrient levels / monocyte differentiation / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / acetyltransferase activity / negative regulation of macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / white fat cell differentiation / cellular response to Thyroglobulin triiodothyronine / positive regulation of double-strand break repair via homologous recombination
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Peroxisome proliferator-activated receptor / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-570 / Chem-L79 / Retinoic acid receptor RXR-alpha / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1 / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHaffner, C.D. / Lenhard, J.M. / Miller, A.B. / McDougald, D.L. / Dwornik, K. / Ittoop, O.R. / Gampe Jr., R.T. / Xu, H.E. / Blanchard, S. / Montana, V.G.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Structure-based design of potent retinoid X receptor alpha agonists.
Authors: Haffner, C.D. / Lenhard, J.M. / Miller, A.B. / McDougald, D.L. / Dwornik, K. / Ittoop, O.R. / Gampe Jr., R.T. / Xu, H.E. / Blanchard, S. / Montana, V.G. / Consler, T.G. / Bledsoe, R.K. / Ayscue, A. / Croom, D.
History
DepositionNov 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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-alpha
B: LxxLL motif coactivator
D: Peroxisome proliferator activated receptor gamma
E: LxxLL motif coactivator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7726
Polymers64,8474
Non-polymers9252
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.69, 54.58, 211.70
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein Retinoic acid receptor RXR-alpha / RXRalpha


Mass: 27114.465 Da / Num. of mol.: 1 / Fragment: ligand binding doamin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: pACYC184 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19793
#3: Protein Peroxisome proliferator activated receptor gamma / PPAR-gamma


Mass: 32557.824 Da / Num. of mol.: 1 / Fragment: ligand binding doamin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231

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Protein/peptide , 2 types, 2 molecules BE

#2: Protein/peptide LxxLL motif coactivator


Mass: 2806.163 Da / Num. of mol.: 1 / Fragment: LxxLL peptide / Source method: obtained synthetically / References: UniProt: Q15788*PLUS
#4: Protein/peptide LxxLL motif coactivator


Mass: 2368.647 Da / Num. of mol.: 1 / Fragment: LxxLL peptide / Source method: obtained synthetically / References: UniProt: Q92793*PLUS

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Non-polymers , 3 types, 207 molecules

#5: Chemical ChemComp-L79 / (S)-(2E)-3[4-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-2-NAPHTHALENYL)TETRAHYDRO-1-BENZOFURAN-2-YL]-2-PROPENOIC ACID


Mass: 378.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30O3
#6: Chemical ChemComp-570 / 2-(2-BENZOYL-PHENYLAMINO)-3-{4-[2-(5-METHYL-2-PHENYL-OXAZOL-4-YL)-ETHOXY]-PHENYL}-PROPIONIC ACID / GI262570 / Farglitazar


Mass: 546.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H30N2O5 / Comment: agonist*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 295 K / pH: 7.5
Details: 17% PEG 4K, 200mM NaSCN, 8% ethylene glycol, 8% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 7.50

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 25137 / % possible obs: 98.6 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 36.9
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.422 / % possible all: 86.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
CNX2000refinement
HKL-2000data scaling
CNX2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FM9

1fm9


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.06 / Data cutoff low absF: 330222 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2121 9.9 %RANDOM
Rwork0.221 ---
obs-21429 97.1 %-
Displacement parametersBiso mean: 41.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 69 205 4030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 359 10.6 %
Rwork0.235 3032 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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