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- PDB-7apo: Crystal structure of RARalpha ligand binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7apo
TitleCrystal structure of RARalpha ligand binding domain in complex with a fragment of the TIF2 coactivator
Components
  • Nuclear receptor coactivator 2
  • Retinoic acid receptor alpha
KeywordsDNA BINDING PROTEIN / Nuclear hormone receptor / coactivator / transcription factor / retinoic acid
Function / homology
Function and homology information


Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / protein kinase B binding / negative regulation of granulocyte differentiation / growth plate cartilage development / glandular epithelial cell development ...Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / 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 / negative regulation of cartilage development / retinoic acid-responsive element binding / regulation of hematopoietic progenitor cell differentiation / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / outflow tract septum morphogenesis / retinoic acid binding / TGFBR3 expression / response to vitamin A / limb development / apoptotic cell clearance / regulation of myelination / Signaling by Retinoic Acid / ureteric bud development / DNA-binding transcription repressor activity / protein kinase A binding / heterocyclic compound binding / positive regulation of interleukin-4 production / alpha-actinin binding / face development / germ cell development / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / cellular response to estrogen stimulus / response to retinoic acid / retinoic acid receptor signaling pathway / cellular response to retinoic acid / positive regulation of cell cycle / response to cytokine / positive regulation of neuron differentiation / mRNA regulatory element binding translation repressor activity / negative regulation of miRNA transcription / liver development / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / female pregnancy / neural tube closure / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / transcription coactivator binding / multicellular organism growth / regulation of synaptic plasticity / Nuclear Receptor transcription pathway / chromatin DNA binding / mRNA 5'-UTR binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / nuclear receptor activity / sequence-specific double-stranded DNA binding / response to estradiol / actin cytoskeleton / cellular response to lipopolysaccharide / spermatogenesis / transcription regulator complex / response to ethanol / cell differentiation / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / protein phosphorylation / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / dendrite / chromatin binding / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Retinoic acid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator ...: / : / Retinoic acid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / 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 / Nuclear receptor coactivator 2 / Retinoic acid receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Authorsle Maire, A. / Guee, L. / Bourguet, W.
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 19, 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

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid receptor alpha
B: Retinoic acid receptor alpha
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1738
Polymers62,2864
Non-polymers8874
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-41 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.694, 47.573, 120.999
Angle α, β, γ (deg.)90.000, 96.169, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Retinoic acid receptor alpha / RAR-alpha / Nuclear receptor subfamily 1 group B member 1


Mass: 28078.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARA, NR1B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10276
#2: Protein/peptide Nuclear receptor coactivator 2


Mass: 3064.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2 / Production host: Escherichia coli (E. coli) / References: UniProt: E7EWM1
#3: 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.: 2 / Source method: obtained synthetically / Formula: C22H25NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Lithium Chloride, 0.1M MES pH6.0, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→46.96 Å / Num. obs: 22707 / % possible obs: 93.85 % / Redundancy: 2.4 % / Biso Wilson estimate: 39.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05802 / Net I/σ(I): 9.35
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 0.2506 / Num. unique obs: 2250 / CC1/2: 0.923

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMR

3kmr


Resolution: 2.4→46.96 Å / SU ML: 0.2611 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2407 1080 4.76 %
Rwork0.1852 21606 -
obs0.1877 22686 93.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 64 129 4198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924167
X-RAY DIFFRACTIONf_angle_d0.85415654
X-RAY DIFFRACTIONf_chiral_restr0.0547673
X-RAY DIFFRACTIONf_plane_restr0.0049716
X-RAY DIFFRACTIONf_dihedral_angle_d20.91361585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.29071410.25332670X-RAY DIFFRACTION93.95
2.51-2.640.27611390.23582617X-RAY DIFFRACTION91.81
2.64-2.810.26641320.21242796X-RAY DIFFRACTION97.34
2.81-3.020.29761670.21392728X-RAY DIFFRACTION97.34
3.02-3.330.23561250.20862750X-RAY DIFFRACTION95.93
3.33-3.810.2141230.1692649X-RAY DIFFRACTION91.45
3.81-4.80.20651200.15122773X-RAY DIFFRACTION95.1
4.8-46.960.23511330.1732623X-RAY DIFFRACTION88.39
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)
13.39053074764-2.05913006124-5.434514702372.378015121773.561724651598.819718115490.2955866241580.5520243304710.238140576213-1.0563037130.2561281615120.71208991523-0.0833174030574-1.2346926982-0.5376187503670.6549497184190.127825469694-0.08836712410270.785254800510.05128716149450.553913530252-39.64956950458.64555199254-42.0437565288
29.864715949960.4100684493184.055202456197.018011854792.538153532945.210280686930.2686473488440.585897548341-0.842269265181-0.8369886813-0.215403232910.1656451325570.5856720256690.253624242651-0.1391867772160.7903455976940.04047833597660.04788212848420.3743813419460.08054038527810.341109846938-18.3598848066-9.3007148103-49.986263642
38.12248800488-5.68312203941-3.568015253817.194825644532.057252031013.953635577850.1001550168540.373309995838-0.0312852747396-0.49818432467-0.203263531095-0.117031903309-0.132442446013-0.2478462307860.07798274890380.542651845022-0.0234293124597-0.02193918323490.3982875473560.02155739277070.193999022465-20.45789374545.73583584809-49.6321244312
41.262673944730.6710343139630.2336880659734.219930945282.174335357321.03986569250.08490978028990.1151824512640.0880070192288-0.430851987026-0.00639250675861-0.180726619511-0.321707626786-0.103523786038-0.08868031668060.5759178537870.0367519289373-0.004088432672940.3271840883170.03086609497710.173283508391-24.684456439813.0165400288-39.6760777225
54.39227808512-6.305431023981.577581491459.12095802184-2.595335335932.20544929078-0.0190405564969-0.0565780346641-0.379837112801-0.2446408057930.1528695649490.2750026107960.4763018721720.390738788821-0.1116732069050.704817721567-0.06651340912830.02973315796650.366740707312-0.04050869721710.312842611432-24.9141277216-11.9606792764-43.3637567968
62.700094593850.535954992629-1.485867133421.811018642441.428055202225.96895158158-0.0332636219321-0.287595948625-0.289421423599-0.125217920491-0.004353149696-0.1061633045180.3330463288030.111705163338-0.007111856458270.4100906008140.0497625387734-0.06956123043070.2290317475330.03828381209150.260598806775-18.7168142505-7.24698908937-40.6667274195
73.993554714524.184047959992.1157036617.367576139292.936168612528.60071880870.2657514560820.106650377962-0.3587951033990.246972995763-0.204058970451-0.62697854398-0.219160435105-0.0273369650896-0.2039972179660.4510281925090.0761343187735-0.05343601700290.3343785150470.0115280925220.313943321409-28.487776472910.5614110536-34.1019180398
87.540764286654.857085418340.8108366144354.260618848931.06899326373.352307566750.831277661933-0.768240844435-0.4442468363481.11187032447-0.860340353615-0.282530970425-0.182712793018-0.363381605636-0.02580751505030.4403424104230.02619833832730.03133549339830.4653417952810.00495915636750.314446656849-37.43853421318.39508708109-28.5942370243
94.224881086751.81430801966-5.966750191392.80431634755-2.563802564678.27133458637-0.332375523745-1.23404953631-0.780563897176-0.0562515714172-0.162641126007-0.5304958809020.1684998467450.8289684080780.4355748262250.5795766476720.0368354729143-0.1440791581140.410165479767-0.03244209424020.407348150986-17.81409858992.50523456026-32.8307315852
104.99130051666-5.73003053582-2.586793961766.544985991113.323423696176.78653982094-0.2694579080620.3686289482790.7985534922530.1362154665470.618540621348-1.423730050310.4327692483590.236804175029-0.5018170368970.639114335937-0.100226018589-0.009901356078630.41590793531-0.03189505779750.375771057018-9.7217496068510.1731037234-46.9688065034
115.596853131965.471631893192.66407560799.379842041281.155961699496.880222993170.60434902491-3.07736659719-0.424575526481.61387789515-0.6930365055680.3175936582590.0524394313297-1.287792752680.06557202758630.574279861958-0.08787267928110.09717305319420.7137366712310.01769459208270.471790526748-27.70972962661.13873756932-3.27414250317
125.409047666732.026346619-4.095651204389.58823124985-0.7734097892357.659167161410.6811528940780.08107029916790.678660854410.899885652365-0.388290231917-0.027491846758-1.53054624883-0.023512373708-0.3827409392710.5842812161030.0556003158614-0.1921328427230.3167258801240.06242846009740.49170678991-4.4144607698719.743080457-9.80537410533
131.229242742391.659452934920.6686097193036.5865007151-0.3970165659251.365115693190.103161719866-0.0996096237961-0.1847767416370.3480087101790.0363541195718-0.170026603980.213585185252-0.0135105597792-0.1576729662080.2902293867760.0269617484982-0.0705334008380.2993415052030.02081663551070.198611440717-11.36695883891.18239980236-11.3560282602
144.98860450109-6.414707831215.412901808078.4273743585-7.087595291375.97896275309-0.562769627493-0.1112852658460.8920609888750.802993862503-0.0717082204416-0.538180140775-0.8717573605180.1434285165070.6637750723480.524876626995-0.0179886210044-0.1243059729680.403096110831-0.01508764818260.415168863587-11.488629864120.2835598781-9.36933365188
158.45222922578-2.5681580422.986891102882.511469898780.4241476198143.24107615855-0.1752561784230.5502067298050.377140090759-0.244051910755-0.142142363537-0.122387333531-0.3686353745230.156161246370.2539032305290.350517915549-0.0390973283099-0.05679895941830.2878210569830.07637195746810.277532250708-11.165339070718.1752052431-18.502249899
169.52663917462-5.93459272472-3.616827611379.568636459875.485419513377.216915282570.5839133165040.2913822466520.0616855034141-0.402605535147-0.273719639176-0.5893575390610.213930424565-0.603873378597-0.3619818877460.467175081579-0.0651839184336-0.1212247344240.3716095117110.09965475180830.241991846997-22.2477381449-0.156121845571-16.141306446
178.56487622711-3.28471960927-0.2514745133614.054373479971.443247328316.969039283810.368258066087-0.106440101695-0.727863683351-0.65906540591-0.3130815139891.583316431530.0372451199286-0.92479539952-0.07437910847610.25996290833-0.0628819105303-0.1029962246450.4781697802070.06483232434240.421036599077-32.5899353551.15205995603-14.9760994441
188.092023492020.6593742909511.758955160191.30938359844-0.3281471033842.543117524660.129829848560.1185350931010.042442680689-0.254059534729-0.0886572749386-0.101273203982-0.2255151036540.0448607760515-0.1414663242730.5575340332730.0187093332489-0.03377971076180.295309154831-0.0211304044640.242170488512-14.70496371997.84597257125-23.4786351284
193.139730138740.857492992621-4.00445270773.66362836016-4.915082702219.39866356753-0.3683861496530.0956678491262-0.855356202517-0.982815792881-0.130931575496-0.6332555727770.3072942565110.1365323561620.5915980489960.4852029092830.01031014773050.05076737814560.372683058887-0.00736892620670.4604966091910.3615137692140.0575793060918-17.1791546286
205.3834359875-2.86707956263-4.209303427943.44272800625-1.055402550178.99739461391.51202813059-0.3108060997971.78934609224-0.384377870881-0.405098651576-0.766138825091-1.710165451421.22285789899-0.8314994496821.22357543962-0.1352562568430.2008945007250.466630309295-0.1280129846480.583986536337-19.048474881420.6056728158-49.0065403212
218.335931624995.920828956884.200967821274.487936623884.334885239078.20772161332-2.07573612398-1.275431853831.013060833851.4593582753-0.1615301115320.793933921961-3.14196866248-0.7336306857292.293347526311.08766079680.0971452990668-0.2311485171060.486656520502-0.06767611658080.723997338627-28.228320645720.0724637867-55.5182031757
224.27112683976-3.716601152765.469845290218.9902357394-5.491282150657.1297651011-0.1057340588220.7557041021240.614601934966-0.0707219936925-0.251623321597-0.441176641873-0.04698943717071.153370773230.3266216378440.568770561441-0.05669358386440.05090015565480.571646660037-0.01600564074560.222756896799-19.661280120514.648385356-57.9385106369
236.822000208585.355283926451.035102089524.664550150272.780445181088.552716428031.12027899676-1.19544500646-2.098023752560.7001139430510.251107577175-1.09789478069-0.2126875702310.43289997292-0.7363551618590.557877511545-0.0182184142064-0.2658844274140.3982572249060.01665269567420.816585482256-5.80507116713-10.3781983849-9.30955150935
245.308951008260.5784293100065.125950930529.11951203584.643850985378.390069357980.661674698974-0.212463533144-0.6713972197970.8310565225350.07354175529451.039546632682.23569822468-3.43320227915-0.8495012589970.957030575622-0.277996987547-0.05986742541671.268488553180.5032876583410.500495974713-8.7866850435-9.318271784981.8418907471
256.71325415267-1.74455379283-2.862356575937.76241001599-3.366218810017.29916063854-0.2527608789940.266570577669-0.0644814365319-0.3623171740190.2588110179870.01018524122560.7470898941641.222174845870.0310408299870.4645543723280.0341267382561-0.1996310999280.475811409959-0.02445049716140.391844420247-0.987983087299-4.61383132206-1.95009315467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 183 through 198 )
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 221 )
3X-RAY DIFFRACTION3chain 'A' and (resid 222 through 245 )
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 275 )
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 285 )
6X-RAY DIFFRACTION6chain 'A' and (resid 286 through 319 )
7X-RAY DIFFRACTION7chain 'A' and (resid 320 through 344 )
8X-RAY DIFFRACTION8chain 'A' and (resid 345 through 372 )
9X-RAY DIFFRACTION9chain 'A' and (resid 373 through 401 )
10X-RAY DIFFRACTION10chain 'A' and (resid 402 through 415 )
11X-RAY DIFFRACTION11chain 'B' and (resid 182 through 198 )
12X-RAY DIFFRACTION12chain 'B' and (resid 199 through 221 )
13X-RAY DIFFRACTION13chain 'B' and (resid 222 through 276 )
14X-RAY DIFFRACTION14chain 'B' and (resid 277 through 290 )
15X-RAY DIFFRACTION15chain 'B' and (resid 291 through 319 )
16X-RAY DIFFRACTION16chain 'B' and (resid 320 through 344 )
17X-RAY DIFFRACTION17chain 'B' and (resid 345 through 372 )
18X-RAY DIFFRACTION18chain 'B' and (resid 373 through 401 )
19X-RAY DIFFRACTION19chain 'B' and (resid 402 through 416 )
20X-RAY DIFFRACTION20chain 'C' and (resid 687 through 694 )
21X-RAY DIFFRACTION21chain 'C' and (resid 695 through 700 )
22X-RAY DIFFRACTION22chain 'C' and (resid 701 through 712 )
23X-RAY DIFFRACTION23chain 'D' and (resid 687 through 694 )
24X-RAY DIFFRACTION24chain 'D' and (resid 695 through 700 )
25X-RAY DIFFRACTION25chain 'D' and (resid 701 through 654 )

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