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- PDB-7aos: crystal structure of the RARalpha/RXRalpha ligand binding domain ... -

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Basic information

Entry
Database: PDB / ID: 7aos
Titlecrystal structure of the RARalpha/RXRalpha ligand binding domain heterodimer in complex with a fragment of SRC1 coactivator
Components
  • (Retinoic acid receptor ...) x 2
  • Nuclear receptor coactivator 1
KeywordsHORMONE / Transcription factor / Nuclear hormone receptor / coactivator / agonist / complex
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 / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of binding / 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 / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of binding / 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 / ventricular cardiac muscle cell differentiation / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / mesenchyme development / Endogenous sterols / positive regulation of translational initiation by iron / chondroblast differentiation / embryonic camera-type eye development / maternal placenta development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein kinase B binding / negative regulation of granulocyte differentiation / growth plate cartilage development / glandular epithelial cell development / positive regulation of T-helper 2 cell differentiation / prostate gland development / Regulation of lipid metabolism by PPARalpha / negative regulation of cartilage development / retinoic acid-responsive element binding / 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 / angiogenesis involved in coronary vascular morphogenesis / cardiac muscle cell differentiation / outflow tract septum morphogenesis / camera-type eye development / retinoic acid binding / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway / response to vitamin A / limb development / apoptotic cell clearance / regulation of myelination / Signaling by Retinoic Acid / ureteric bud development / cardiac muscle cell proliferation / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity / protein kinase A binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear steroid receptor activity / hypothalamus development / ventricular cardiac muscle tissue morphogenesis / male mating behavior / heterocyclic compound binding / positive regulation of interleukin-4 production / alpha-actinin binding / face development / germ cell development / negative regulation of type II interferon production / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor production / cellular response to estrogen stimulus / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of bone mineralization / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / heart morphogenesis / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity
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 receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking ...: / : / Retinoic acid receptor / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 1 / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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 / 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-EQN / Chem-LG2 / Retinoic acid receptor alpha / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
Authorsle Maire, A. / Guee, L. / Bourguet, W.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR).
Authors: Senicourt, L. / le Maire, A. / Allemand, F. / Carvalho, J.E. / Guee, L. / Germain, P. / Schubert, M. / Bernado, P. / Bourguet, W. / Sibille, N.
History
DepositionOct 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor alpha
C: Nuclear receptor coactivator 1
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5657
Polymers62,7584
Non-polymers8073
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-27 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.283, 108.283, 99.786
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

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Components

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Retinoic acid receptor ... , 2 types, 2 molecules AB

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


Mass: 26579.727 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 (bacteria) / References: UniProt: P28700
#2: Protein Retinoic acid receptor alpha / RAR-alpha / Nuclear receptor subfamily 1 group B member 1


Mass: 29967.590 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 (bacteria) / References: UniProt: P10276

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 3105.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase

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Non-polymers , 4 types, 16 molecules

#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EQN / 4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid


Mass: 351.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 24% PEG 3350, 0.2M Na acetate, 0.1M Bis Tris Propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.55→48.43 Å / Num. obs: 19916 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 60.09 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.83
Reflection shellResolution: 2.55→2.641 Å / Num. unique obs: 1960 / CC1/2: 0.651

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHASER1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xdk + 3kmr

1xdk

3kmr


Resolution: 2.55→48.43 Å / SU ML: 0.3712 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8441
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2623 1995 10.02 %
Rwork0.205 17919 -
obs0.2109 19914 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.71 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3713 0 59 13 3785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223853
X-RAY DIFFRACTIONf_angle_d0.51045224
X-RAY DIFFRACTIONf_chiral_restr0.0366605
X-RAY DIFFRACTIONf_plane_restr0.003660
X-RAY DIFFRACTIONf_dihedral_angle_d10.4596523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.35781380.29541247X-RAY DIFFRACTION100
2.61-2.680.32741460.28551251X-RAY DIFFRACTION100
2.68-2.760.37521370.2831256X-RAY DIFFRACTION100
2.76-2.850.34321480.27061264X-RAY DIFFRACTION99.93
2.85-2.950.3251300.27081259X-RAY DIFFRACTION99.93
2.95-3.070.33381350.26031261X-RAY DIFFRACTION100
3.07-3.210.28251420.25511247X-RAY DIFFRACTION100
3.21-3.380.36651440.24561274X-RAY DIFFRACTION100
3.38-3.590.30531390.23081280X-RAY DIFFRACTION100
3.59-3.870.26421420.19741286X-RAY DIFFRACTION100
3.87-4.260.2171460.17191273X-RAY DIFFRACTION99.93
4.26-4.880.20281440.15511294X-RAY DIFFRACTION99.93
4.88-6.140.24121460.20071324X-RAY DIFFRACTION100
6.14-48.430.2261580.17151403X-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)
14.52351542262-0.1168452008151.373483178264.57272788205-0.9459334842611.018096839120.403494228585-0.294440908871-0.974320102933-0.08614928146420.000634059809682-0.2693788187431.8009541888-0.7529342858990.02404130268810.799280500699-0.1197707429940.07117824049490.656132268614-0.0518474839160.67776622242921.6587202738-34.2359623679-5.72858842868
21.78333004181.091977075960.8015250068460.6211409282790.09663440109742.43405296501-0.5319638192740.3476436836520.693185141658-0.1201793977390.515462772174-0.291151493919-1.77070090271-1.6051950097-0.1903966610341.654168043350.1636799791630.07142245945961.665794752630.1470962769711.06049182296-0.31610471927-15.038889752-23.9165250473
33.056502489961.02166114827-0.2058342779952.992319869940.3432199065216.70966403253-0.1494948120720.0615350207667-0.258447924425-0.03395376657540.03056592201840.318258653758-0.0397571362253-2.50717560213-0.01880136927890.4635127086090.1047272472360.009208090616541.1124487628-0.07403651479150.5212313284788.94150134919-22.303303913-7.82921537849
43.98733551644-0.22982826215-0.2123154750543.931251231560.9384593683125.122866841410.2025959994120.1858242352630.0373889435353-0.0555067301701-0.2822326794610.13440398522-0.30557553021-0.5892519621380.05991260533170.4212977089840.0638315636708-0.04965409302190.477749587583-0.07133848610070.32643295659520.3299703376-18.89687157-4.77822132853
56.69547108908-2.403891099670.6793484284936.07369938525-2.666586038771.47542090138-0.5213952444-0.2775649247230.3895150131290.5135790748950.5055291633980.737587126037-0.95027011768-1.91984342457-0.04161009117750.7834384969370.4488893784420.0467190197371.46395469911-0.1408316600880.5131462708369.01204315354-13.5243428078-3.13288105161
66.53902916366-4.68019559085-3.288320923758.934238050943.053247043034.29043544412-0.36246533310.292530627977-0.01623931210350.6954845641390.197073091071-0.7369802329740.6634386535310.6441016720970.08194145141960.5239495020010.0862683366011-0.09932088881740.51459695203-0.08838198315080.63733118860943.7470802766-12.019134504211.2808314661
76.367401174640.208715238029-2.501834974943.734902016420.2356361924825.96134067050.153139909327-0.8383463886390.2936893512710.689329277517-0.1519257173330.4144542686890.06087127344940.0215874962601-0.06007397060520.538977064069-0.1212100398020.04104251021950.439184113203-0.03377611210650.49808220607923.07184391553.1269730087123.8576738342
83.744707591910.665372447168-2.17251962094.03083034213-0.06265393665725.160407635510.235733971693-0.1898833743730.09048994180080.160393571303-0.07400904215670.1365788806090.278482037460.0624046626623-0.06702568117750.372409595213-0.067563471736-0.04020554609820.337500594605-0.01232375201960.39486929831224.5946450909-1.6615236587416.8452373198
97.0275194561.63718027487-3.244688541962.404906496581.872522518655.677116734580.365896255918-0.137365300654-0.1630449078870.443770642173-0.2583940607420.06592718985870.10372666011-0.245257539341-0.1807701316590.511972372863-0.0523732094304-0.0612096614330.319350689621-0.03493536730920.43567223531525.3924161349-8.3772349083310.7903550726
107.16130326094-3.163580873921.718429266982.9759583834-1.386367281468.403157813760.4509377142160.0446844797504-0.595737212672-0.774738657823-0.138484870804-0.3228433892160.9455913607831.0334090816-0.3114375871630.570820359450.0355814040522-0.1208533681920.510356959124-0.1036414089940.65108891970936.3391022399-15.03303379644.77486310542
113.976872924330.9374718863430.09079229986132.80646783060.7515075010433.330150746210.01140439280850.3064967998580.3539124200570.373974928099-0.2415770342760.8504330699790.036017770613-0.4143156291110.3543350609110.372999257181-0.0180172028972-0.001687919161560.469034879637-0.007284694611240.45453884148918.6957052342-2.4648990972610.7316197263
124.99053239036-5.13337369067-0.6590563222425.384853898151.140366312622.14129003406-0.05202445910411.527965872511.25686247913-1.45028306927-0.330334216839-0.7898166963530.0648335744302-0.5818385559080.1457198533050.871782597813-0.128693990671-0.1345005765320.654290827740.08877757895630.54999612867130.875409367314.08289697585.90352448605
136.06054989658-5.45822689152-3.692880126235.080734248542.333561201468.279316515370.04352652589-2.23328510136-1.645878996320.654169357365-0.3085387911671.125185368942.22076068592-0.3371919475960.2966105733950.575377932183-0.868449263754-0.0167694247352.150639024580.05826637869790.771180829392-1.05827832606-31.589586269-1.62155562937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 241 )
2X-RAY DIFFRACTION2chain 'A' and (resid 242 through 263 )
3X-RAY DIFFRACTION3chain 'A' and (resid 264 through 330 )
4X-RAY DIFFRACTION4chain 'A' and (resid 331 through 413 )
5X-RAY DIFFRACTION5chain 'A' and (resid 414 through 456 )
6X-RAY DIFFRACTION6chain 'B' and (resid 175 through 198 )
7X-RAY DIFFRACTION7chain 'B' and (resid 199 through 245 )
8X-RAY DIFFRACTION8chain 'B' and (resid 246 through 302 )
9X-RAY DIFFRACTION9chain 'B' and (resid 303 through 344 )
10X-RAY DIFFRACTION10chain 'B' and (resid 345 through 370 )
11X-RAY DIFFRACTION11chain 'B' and (resid 371 through 415 )
12X-RAY DIFFRACTION12chain 'C' and (resid 686 through 696 )
13X-RAY DIFFRACTION13chain 'D' and (resid 689 through 695 )

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