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

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Basic information

Entry
Database: PDB / ID: 7pdt
TitleCrystal structure of a mutated form of RXRalpha ligand binding domain in complex with BMS649 and a coactivator fragment
Components
  • Nuclear receptor coactivator 2
  • Retinoic acid receptor RXR-alpha
KeywordsNUCLEAR PROTEIN / nuclear hormone receptor / ligand binding
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-BM6 / 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: 3.3 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 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
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
U: Nuclear receptor coactivator 2
B: Retinoic acid receptor RXR-alpha
V: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2996
Polymers57,5404
Non-polymers7592
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-12 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.392, 68.526, 109.717
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 27190.346 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-BM6 / 4-[2-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-NAPHTHALEN-2-YL)-[1,3]DIOXOLAN-2-YL]-BENZOIC ACID / BMS649


Mass: 379.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C24H27O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG3350, 0.2M Na Nitrate, 0.1M BisTris propane pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 3.3→42.84 Å / Num. obs: 7562 / % possible obs: 98.94 % / Redundancy: 4.9 % / Biso Wilson estimate: 83.5 Å2 / CC1/2: 0.994 / Net I/σ(I): 10.77
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 965 / CC1/2: 0.491

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
autoPROC1.18.2_3874data processing
SCALAdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+94 / Resolution: 3.3→42.84 Å / SU ML: 0.2839 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2075 761 10.1 %
Rwork0.1924 6770 -
obs0.194 7531 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.22 Å2
Refinement stepCycle: LAST / Resolution: 3.3→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 56 7 3491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313554
X-RAY DIFFRACTIONf_angle_d0.6584817
X-RAY DIFFRACTIONf_chiral_restr0.0399558
X-RAY DIFFRACTIONf_plane_restr0.0041633
X-RAY DIFFRACTIONf_dihedral_angle_d14.86181351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.550.26331700.25651309X-RAY DIFFRACTION99.4
3.56-3.910.23571420.20771335X-RAY DIFFRACTION99.06
3.91-4.480.19131380.17841342X-RAY DIFFRACTION99.06
4.48-5.640.21021660.18521345X-RAY DIFFRACTION99.21
5.64-42.840.1811450.18091439X-RAY DIFFRACTION98.32
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)
11.22623248629-0.296611287483-1.535895962810.648428764457-0.2908542035982.57107964578-0.267921177497-0.200470609474-0.05759065098770.430656642613-0.124521743142-0.139381206389-0.644731728912-0.1098982352130.3248017681830.47215480449-0.079465423005-0.07235270000370.732374462241-0.08803348307350.45472542826227.555321818345.234626881245.7473634687
22.95174138479-0.110410202582-1.065709562272.89585383992-2.096500764163.156785378340.0110279843181-0.01408976962580.2194391803820.137688026482-0.01951502300650.151218393161-0.280131451042-0.2489978209160.05969754363510.5738265661980.0462489374244-0.002844160591680.596931546945-0.007593416932150.5135268089538.020470843651.175318964745.1213174023
32.500283987691.52848180566-1.745142489762.8394868886-0.4621506989263.8601128209-0.2200063096870.561774995173-0.230870442856-0.1032715462110.0253722697884-0.05370673692620.272532753336-0.6358725952920.1351028964850.5065059845850.007241892344010.009743064333410.760350989656-0.04044960780230.47510140366237.770520346640.262849582639.703217368
44.17120019631.25644508673-0.1312952180815.288112750990.8605205151592.57211652378-0.04955417199980.24681635651-0.2875583330990.0336019262242-0.0351773757755-0.541398524896-0.07249458781420.09704767518230.2212200612470.6471876710280.0207196622804-0.02312157020720.6584654552060.02121283557450.56364164382446.886889646144.13701149239.2234586974
52.215579812751.38884707433-2.673903347518.86686196596-0.4151388312379.505276496260.306049134363-1.68691844511.136056697260.492082464435-0.266929629911-0.9735980806990.07642306956030.693581338366-0.02857848146180.6424524795130.0766636685463-0.1265123021520.7586509795770.0257399248750.95755295417248.481899578860.572201523947.6344496741
64.97396241354-2.242801069123.83129174952.988245687750.2063890876437.124096438680.0262132912546-0.7934191937131.022335985510.605151261855-0.371738117803-1.01798804476-0.000473514455177-0.313079109423-0.1068396771340.483876820717-0.08184094969930.1521579930930.838835458685-0.1204462614660.79451033660239.763096451256.547153261559.6428196822
73.042988300770.6139372786833.647130800242.390771404550.8530981529215.66585685835-0.2859268953840.584589602158-0.695857235124-0.3196025138670.312760174428-0.2042619232980.1825665909230.3629731385880.08200892243590.581428554205-0.02945105301130.06404870039410.574144683644-0.1527638979850.62158747627959.402799923223.949681154734.4511064291
84.6996757523-0.328166031635-0.3190556866033.311408009510.7958530505940.554724862830.211505299454-0.272103500063-0.3099840272930.103981703027-0.03034926005810.1260373292330.461820404139-0.100619219302-0.1808177991550.730025010365-0.03702392637120.02671890716590.6208526213250.07572006092640.55600192055960.129463458828.300491621852.7396521077
93.948682812821.77288399569-0.8888558137714.77373667952-0.8079074843182.13510425031-0.1837426415580.689630189504-0.4179247245420.2633391810730.1692632764690.3538559767480.314642267274-0.7364029128920.0141427163670.718186320596-0.173812086350.061596313750.769135090317-0.1393719341870.51685731997944.645704825523.618939185234.9438675643
106.814025438092.83851699899-1.981546889814.824652945870.9601159254672.757899308020.3298231258260.4092094661550.1249452188230.8038496028020.09142421468640.0486568298983-0.0805063908796-0.00593244530972-0.5245785889190.6144794686750.06228031719920.04262550976050.568934850178-0.002199873221140.43365720616755.964783515135.77388984942.4026745659
113.64742979897-3.514890214771.614953024714.76651735569-3.294236832092.87814491232-0.4227461903181.824227064530.706579105873-0.155877963546-0.591148475492-1.393149708930.4765817968241.525598988960.7626851536720.756199122043-0.1782507458760.08245787456570.800643170134-0.03748984203490.72626541215171.793050371735.617666001834.3788297541
124.76913906622-5.68580042436-0.9151969915047.08141196030.2841183056782.28480083196-0.4650863313480.9019305496010.0441729595197-0.4147401153510.196263183255-0.585653091280.0907197333757-1.83784992370.1523106828420.6723365388040.05336652560970.1968235382191.11739136273-0.1279501257970.71421272002867.305084029927.09011161122.6902974064
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 234 through 268 )AB234 - 2681 - 16
22chain 'A' and (resid 269 through 335 )AB269 - 33517 - 83
33chain 'A' and (resid 336 through 416 )AB336 - 41684 - 164
44chain 'A' and (resid 417 through 447 )AB417 - 447165 - 195
55chain 'A' and (resid 448 through 461 )AB448 - 461196 - 209
66chain 'U' and (resid 250 through 260 )UC250 - 2601 - 11
77chain 'B' and (resid 234 through 323 )BE234 - 3231 - 70
88chain 'B' and (resid 324 through 368 )BE324 - 36871 - 115
99chain 'B' and (resid 369 through 418 )BE369 - 418116 - 165
1010chain 'B' and (resid 419 through 447 )BE419 - 447166 - 194
1111chain 'B' and (resid 448 through 461 )BE448 - 461195 - 208
1212chain 'V' and (resid 301 through 309 )VF301 - 3091 - 9

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