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- PDB-7pdq: Crystal structure of a mutated form of RXRalpha ligand binding do... -

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Basic information

Entry
Database: PDB / ID: 7pdq
TitleCrystal structure of a mutated form of RXRalpha ligand binding domain in complex with LG100268 and a coactivator fragment
Components
  • Nuclear receptor coactivator 2
  • Retinoic acid receptor RXR-alpha
KeywordsNUCLEAR PROTEIN / nuclear hormone receptor
Function / homology
Function and homology information


Transcriptional regulation of granulopoiesis / Carnitine metabolism / Transcriptional regulation of white adipocyte differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / 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 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol ...Transcriptional regulation of granulopoiesis / Carnitine metabolism / Transcriptional regulation of white adipocyte differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / 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 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Nuclear Receptor transcription pathway / Synthesis of bile acids and bile salts / ventricular cardiac muscle cell differentiation / visceral serous pericardium development / mesenchyme development / positive regulation of translational initiation by iron / Endogenous sterols / maternal placenta development / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / Regulation of lipid metabolism by PPARalpha / retinoic acid-responsive element binding / Cytoprotection by HMOX1 / positive regulation of thyroid hormone mediated signaling pathway / angiogenesis involved in coronary vascular morphogenesis / cardiac muscle cell differentiation / nuclear retinoic acid receptor binding / anatomical structure development / ion binding / camera-type eye development / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / nuclear thyroid hormone receptor binding / cardiac muscle cell proliferation / regulation of myelination / ventricular cardiac muscle tissue morphogenesis / DNA binding domain binding / nuclear steroid receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / 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 / heart morphogenesis / response to retinoic acid / response to glucocorticoid / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / embryo implantation / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / placenta development / response to progesterone / transcription coregulator binding / nuclear receptor binding / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / gene expression / heart development / HATs acetylate histones / double-stranded DNA binding / Estrogen-dependent gene expression / in utero embryonic development / transcription regulator complex / sequence-specific DNA binding / cell differentiation / transcription coactivator activity / receptor complex
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / 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. / Nuclear receptor coactivator, interlocking / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
Similarity search - Domain/homology
Chem-LG2 / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
Authorsle Maire, A. / Bourguet, W. / Guee, L.
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
DepositionAug 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Aug 17, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2193
Polymers28,8552
Non-polymers3631
Water5,999333
1
A: Retinoic acid receptor RXR-alpha
B: Nuclear receptor coactivator 2
hetero molecules

A: Retinoic acid receptor RXR-alpha
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4386
Polymers57,7114
Non-polymers7272
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)68.430, 68.430, 105.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-743-

HOH

21A-842-

HOH

31A-900-

HOH

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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: 27275.402 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/peptide Nuclear receptor coactivator 2 / / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-LG2 / 6-[1-(3,5,5,8,8-PENTAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)CYCLOPROPYL]PYRIDINE-3-CARBOXYLIC ACID


Mass: 363.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 26% PEG3350, 0.2M NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.579→48.39 Å / Num. obs: 34564 / % possible obs: 98.25 % / Redundancy: 22 % / Biso Wilson estimate: 19.68 Å2 / CC1/2: 1 / Net I/σ(I): 32.76
Reflection shellResolution: 1.579→1.635 Å / Num. unique obs: 2903 / CC1/2: 0.812

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Processing

Software
NameVersionClassification
Coot1.18.2_3874model building
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6sti

6sti


Resolution: 1.58→48.39 Å / SU ML: 0.157 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1954 1708 4.94 %
Rwork0.1723 32849 -
obs0.1734 34557 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.86 Å2
Refinement stepCycle: LAST / Resolution: 1.58→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 27 333 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01581828
X-RAY DIFFRACTIONf_angle_d1.62012482
X-RAY DIFFRACTIONf_chiral_restr0.0915281
X-RAY DIFFRACTIONf_plane_restr0.0093312
X-RAY DIFFRACTIONf_dihedral_angle_d21.0645690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.630.31391030.27112234X-RAY DIFFRACTION81.2
1.63-1.680.20851520.20232667X-RAY DIFFRACTION97.95
1.68-1.740.20451260.19382733X-RAY DIFFRACTION99.58
1.74-1.810.21011460.18212731X-RAY DIFFRACTION99.93
1.81-1.890.20981570.17322738X-RAY DIFFRACTION100
1.89-1.990.19311450.18112756X-RAY DIFFRACTION100
1.99-2.110.21281540.17642748X-RAY DIFFRACTION100
2.11-2.280.16891390.16752775X-RAY DIFFRACTION100
2.28-2.510.17941540.16752783X-RAY DIFFRACTION100
2.51-2.870.20581530.18072805X-RAY DIFFRACTION100
2.87-3.610.20341320.16632862X-RAY DIFFRACTION100
3.62-48.390.17911470.15943017X-RAY DIFFRACTION99.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.12249605438-2.01225495033-1.770669850371.677964303250.4812526897721.323356170970.1199466580580.1152102139380.187757163175-0.000620377153836-0.05095661035970.0598360032826-0.0735857671946-0.138650770941-0.08229250183860.141416388339-0.0126630063398-0.02161443788890.0948774067831-0.009231670400040.0953455922514-15.46657614991.03557641489-25.6594965591
27.265500572670.9799943272311.668964921252.712448737343.10372920014.17146726026-0.269002707007-0.6053623231480.3790342391680.5883247531490.05040575093740.046396899381-0.2299420551080.07453378599690.1292568352010.229178954384-0.04117900728030.01927345653250.2645235432950.005500368695480.212530693774-21.7803023469-8.42547408784-8.70622217188
33.053080876-0.8228512445630.3285971294542.53785925361-1.043594224771.732824679920.0904992959731-0.115065345757-0.4175656217830.01570308575520.01479571653790.1403320567510.316309563401-0.0669511198761-0.1282404340580.190824680368-0.03286798359150.001534375610810.08038986512190.01393365232440.136562143234-14.3233328145-13.7157191015-20.3972063443
41.32247430909-0.292591818911.094927578620.884373798644-0.5290468873152.641515190320.06694988208450.0719011639979-0.0924176416751-0.0931946543984-0.003986668659130.05646915279910.0845526495493-0.0290557917027-0.06087446615820.118781944511-0.0166236702201-0.005131531298570.08262875162260.002310663761290.135599840901-13.7848133115-5.74086484322-32.8700412316
53.31772150627-1.66983787686-1.95774932472.478970689111.710411712163.943030424380.00752568338928-0.186927379319-0.08455948708010.09884726268630.0905784511243-0.1408191495120.2619878452120.22949403239-0.1128849944880.1229920226570.0243822269329-0.02486214727470.08534829116330.03129786670630.1293591695620.548482560754-11.4164815011-21.0749110207
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 419 through 462 )AA419 - 462171 - 216
22chain 'B' and (resid 686 through 697 )BC686 - 6971 - 12
33chain 'A' and (resid 234 through 298 )AA234 - 2981 - 44
44chain 'A' and (resid 299 through 368 )AA299 - 36845 - 120
55chain 'A' and (resid 369 through 418 )AA369 - 418121 - 170

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