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- PDB-7qaa: Crystal structure of RARalpha/RXRalpha ligand binding domain hete... -

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Basic information

Entry
Database: PDB / ID: 7qaa
TitleCrystal structure of RARalpha/RXRalpha ligand binding domain heterodimer in complex with BMS614 and oleic acid
Components
  • Isoform Alpha-1-deltaBC of Retinoic acid receptor alpha
  • Retinoic acid receptor RXR-alpha
KeywordsGENE REGULATION / Nuclear receptor
Function / homology
Function and homology information


Transcriptional regulation of granulopoiesis / Carnitine shuttle / Transcriptional regulation of white adipocyte differentiation / Signaling by Retinoic Acid / Sertoli cell fate commitment / positive regulation of binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of intracellular receptors / trachea cartilage development ...Transcriptional regulation of granulopoiesis / Carnitine shuttle / Transcriptional regulation of white adipocyte differentiation / Signaling by Retinoic Acid / Sertoli cell fate commitment / positive regulation of binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of intracellular receptors / trachea cartilage development / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / visceral serous pericardium development / glandular epithelial cell development / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / ventricular cardiac muscle cell differentiation / mesenchyme development / Endogenous sterols / chondroblast differentiation / positive regulation of translational initiation by iron / embryonic camera-type eye development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / maternal placenta development / protein kinase B binding / negative regulation of granulocyte differentiation / growth plate cartilage development / angiogenesis involved in coronary vascular morphogenesis / prostate gland development / positive regulation of T-helper 2 cell differentiation / Regulation of lipid metabolism by PPARalpha / retinoic acid-responsive element binding / negative regulation of cartilage development / regulation of hematopoietic progenitor cell differentiation / Cytoprotection by HMOX1 / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / positive regulation of thyroid hormone receptor signaling pathway / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / cardiac muscle cell differentiation / retinoic acid binding / camera-type eye development / outflow tract septum morphogenesis / TGFBR3 expression / response to vitamin A / positive regulation of vitamin D receptor signaling pathway / heterocyclic compound binding / limb development / apoptotic cell clearance / regulation of myelination / ureteric bud development / Signaling by Retinoic Acid / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity / regulation of branching involved in prostate gland morphogenesis / protein kinase A binding / ventricular cardiac muscle tissue morphogenesis / positive regulation of interleukin-4 production / alpha-actinin binding / face development / germ cell development / negative regulation of type II interferon production / nuclear steroid receptor activity / negative regulation of tumor necrosis factor production / cellular response to estrogen stimulus / cardiac muscle cell proliferation / response to retinoic acid / positive regulation of bone mineralization / heart morphogenesis / retinoic acid receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of cell cycle / cellular response to retinoic acid / response to cytokine / positive regulation of neuron differentiation / embryo implantation / negative regulation of miRNA transcription / mRNA regulatory element binding translation repressor activity / placenta development / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neural tube closure / SUMOylation of intracellular receptors / chromatin DNA binding / mRNA transcription by RNA polymerase II / liver development / female pregnancy / regulation of synaptic plasticity / mRNA 5'-UTR binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / transcription coactivator binding / multicellular organism growth / Transcriptional regulation of granulopoiesis / nuclear receptor activity / sequence-specific double-stranded DNA binding / response to estradiol
Similarity search - Function
: / : / Retinoic acid receptor / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...: / : / Retinoic acid receptor / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / 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
Similarity search - Domain/homology
Chem-BMS / OLEIC ACID / Retinoic acid receptor alpha / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
Authorsle Maire, A. / Vivat, V. / Guee, L. / Blanc, P. / Malosse, C. / Chamot-Rooke, J. / Germain, P. / Bourguet, w.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Endocrinol. / Year: 2022
Title: Design and in vitro characterization of RXR variants as tools to investigate the biological role of endogenous rexinoids.
Authors: le Maire, A. / Rey, M. / Vivat, V. / Guee, L. / Blanc, P. / Malosse, C. / Chamot-Rooke, J. / Germain, P. / Bourguet, W.
History
DepositionNov 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
B: Isoform Alpha-1-deltaBC of Retinoic acid receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3774
Polymers52,6442
Non-polymers7332
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-5 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.600, 116.600, 207.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha


Mass: 26044.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rxra, Nr2b1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28700
#2: Protein Isoform Alpha-1-deltaBC of Retinoic acid receptor alpha / RAR-alpha / Nuclear receptor subfamily 1 group B member 1


Mass: 26600.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARA, NR1B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10276
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BMS / 4-[(4,4-DIMETHYL-1,2,3,4-TETRAHYDRO-[1,2']BINAPTHALENYL-7-CARBONYL)-AMINO]-BENZOIC ACID


Mass: 450.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H26N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.87 Å3/Da / Density % sol: 68.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 23% PEG 10,000 0.1 M Hepes, pH 7.25

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.918 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 5, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.76→19.47 Å / Biso Wilson estimate: 47.78 Å2
Reflection shellResolution: 2.76→2.86 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dkf

1dkf


Resolution: 2.76→19.82 Å / SU ML: 0.2487 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.2324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245 1009 4.87 %
Rwork0.1947 19728 -
obs0.1971 20737 93.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.51 Å2
Refinement stepCycle: LAST / Resolution: 2.76→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 54 121 3654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523599
X-RAY DIFFRACTIONf_angle_d0.98684876
X-RAY DIFFRACTIONf_chiral_restr0.0545569
X-RAY DIFFRACTIONf_plane_restr0.0053652
X-RAY DIFFRACTIONf_dihedral_angle_d6.7043523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.910.3012960.22212041X-RAY DIFFRACTION69.32
2.91-3.090.2631430.24042779X-RAY DIFFRACTION94.9
3.09-3.330.30421440.23362858X-RAY DIFFRACTION96.78
3.33-3.660.24831620.20382906X-RAY DIFFRACTION98.46
3.66-4.180.20861660.17482948X-RAY DIFFRACTION98.98
4.18-5.250.25071450.16883018X-RAY DIFFRACTION99.37
5.25-19.820.22811530.19263178X-RAY DIFFRACTION98.58

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