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- PDB-7bk4: Crystal structure of RXRalpha ligand binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7bk4
TitleCrystal structure of RXRalpha ligand binding domain in complex with a fragment of the TIF2 coactivator
Components
  • Nuclear receptor coactivator 2
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / Nuclear Receptor / Ligand binding domain / coactivator
Function / homology
Function and homology information


positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex ...positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / 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 / response to retinoic acid / Recycling of bile acids and salts / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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) / nuclear receptor coactivator activity / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / receptor complex / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
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, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein ...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, 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. / 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 / Nuclear receptor coactivator 2 / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
Authorsle Maire, A. / 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
DepositionJan 15, 2021Deposition 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 RXR-alpha
B: Nuclear receptor coactivator 2
C: Retinoic acid receptor RXR-alpha
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3956
Polymers60,6684
Non-polymers7272
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-25 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.132, 64.659, 48.514
Angle α, β, γ (deg.)90.000, 95.283, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: 27269.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19793
#2: Protein/peptide Nuclear receptor coactivator 2


Mass: 3064.559 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: E7EWM1
#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.: 2 / Source method: obtained synthetically / Formula: C24H29NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na Hepes, 0.2 M sodium acetate pH 7.5, 27% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.8→48.31 Å / Num. obs: 13251 / % possible obs: 96.11 % / Redundancy: 3.1 % / Biso Wilson estimate: 30.15 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.0686 / Net I/σ(I): 16.52
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.1866 / Num. unique obs: 1338 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
REFMAC7.1.005refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KWY

3kwy


Resolution: 2.8→48.31 Å / SU ML: 0.3485 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 31.2188
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2654 1958 7.9 %
Rwork0.2456 22826 -
obs0.2473 13243 92.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.16 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 54 69 3764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513780
X-RAY DIFFRACTIONf_angle_d1.37235125
X-RAY DIFFRACTIONf_chiral_restr0.1153583
X-RAY DIFFRACTIONf_plane_restr0.0067644
X-RAY DIFFRACTIONf_dihedral_angle_d23.97151413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.32431630.29471654X-RAY DIFFRACTION95.08
2.87-2.950.33611220.28331680X-RAY DIFFRACTION95.24
2.95-3.030.32671510.27961654X-RAY DIFFRACTION95.1
3.03-3.130.24241230.26891679X-RAY DIFFRACTION95.24
3.13-3.240.34611400.28261738X-RAY DIFFRACTION94.99
3.24-3.370.29941410.28751580X-RAY DIFFRACTION91.88
3.37-3.530.26531390.26941651X-RAY DIFFRACTION93.91
3.53-3.710.23721310.23761642X-RAY DIFFRACTION93.61
3.71-3.950.23491310.23291648X-RAY DIFFRACTION93.53
3.95-4.250.20891670.2131575X-RAY DIFFRACTION91.54
4.25-4.680.23791740.2121546X-RAY DIFFRACTION90.53
4.68-5.350.22781200.22641585X-RAY DIFFRACTION88.43
5.35-6.740.31271250.26081612X-RAY DIFFRACTION91.32
6.75-48.310.27521310.20911582X-RAY DIFFRACTION89.78
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)
16.40689483752-0.7302255000692.693482521290.690463571738-0.1648853825411.86294064771-0.6753932566650.398548002248-1.04236171054-0.01465045858230.374742721701-0.0324741603544-0.535274802980.2628578814040.2505212332690.394661397934-0.0739985187830.1593093802240.4513072673530.1406901864990.3302970269931.6558605644-18.92362308943.12229605004
25.00396754293-2.097252618752.366988727855.426941007080.1498821361365.57681452375-0.530664401398-0.05262868512940.416350737259-0.2409214419960.0287033079725-0.7705933227930.2592901302970.2238939268140.3056891958740.2903531644890.07929679627940.1749389677050.3488853421070.05586000404310.38153500867245.1405110376-15.101038860924.6992224902
30.853878865485-0.7515730591570.8940089650051.238413362880.3592698169714.592849498980.0182989225284-0.0275678790821-0.0356790769853-0.0336061095487-0.0584482431886-0.3593926941590.246894774189-0.02682239618590.02801563230770.246356185955-0.0279232665720.08321549536380.1454297380130.004304015836240.22172198330141.0752509902-6.306774853567.05445811223
40.7209861352150.1199997032661.075268063490.419001790020.2442237041141.856799518310.0734523723903-0.193996615114-0.03857790800530.111582805003-0.03183315817280.1949913054640.198833028748-0.1210049366260.03359110902080.1794401798280.001777336376520.110071033890.246483115950.006667434488510.24434396923532.6174158827-5.4499531018420.8905017071
52.691380351290.507491945344-1.063424560712.88259780091-0.3851136721423.670535034470.2551663755130.0988579473586-0.1198288071310.108958998461-0.1255019634710.3173445973260.000469308180975-0.119127424853-0.1508108531860.185201125559-0.03478764522130.06748039106210.277551208786-0.01499470901410.22020609682924.7548152035-9.00658203780.465002863721
62.440306397751.652600352410.9839399920883.017947942640.3339297896641.768164181440.2096947665340.6616912140080.2969692257630.8005328905130.034802859530.136596086740.1449274374390.0133277316671-0.09933828371610.1361868006430.02176940061530.06421015539170.1955019666750.02686159902560.25592119157931.29168418172.1800292001312.8962814192
72.0144892462-1.22003257064-2.072049767175.608073708132.864843096564.134434566380.3494583998120.202286092130.2985552651480.2299757735150.268956476036-1.128754293920.04516100860140.543550296523-0.3983544060410.126312364440.04696109601270.05003841190050.283778926835-0.06812687773140.38433159934950.63288505354.2909474823311.7920911286
82.302743766021.81316019072.113610988263.27682857507-1.007606629775.79967056062-0.1053345702990.2631399381320.362706441274-0.5995047821970.201608288566-0.2829792524560.07571319601120.699230807712-0.1398775965720.1882967307050.05296015846540.1385727791610.272506007267-0.03271295975450.34946550021451.0146157008-3.12096812157-0.984046109318
92.659334961070.05151896386530.6117020968694.90549285844-2.22500299883.01444426619-0.2216583005210.430676702773-0.4193387938071.02427805363-0.11073709061-0.9288836715471.0263962270.3046516383070.06276659561650.6222421967710.06342055605780.02780007674470.288400252692-0.08058143306630.41874154694944.9826812998-12.9827532974-11.0179269528
102.692616630351.24177819507-1.013165439861.845456791860.3819218989221.231835095350.141831792795-0.0459159752810.1929718685150.180589940412-0.05845290068420.242227930348-0.323277150809-0.6524679071510.01822161465390.182753005146-0.01933977808930.005223770875970.3903296715310.1158857762030.4905800353029.5023951499117.58336418376.00209909008
112.523857008660.3956115069691.281238986292.957287392490.2077578764530.7673624710930.036623229360.009629674312410.2006688387810.3062088158730.05049880156130.11121412949-0.10082502512-0.0679785112028-0.04867123603420.1229589816460.00171606191750.1154823945320.3013405486740.02588670049010.30973741377614.467454000315.1468994647.34357088528
120.769879953151.28163153320.1817014692813.04366255752-0.280988520910.286820400434-0.1447907744630.2361336683380.0771435675935-0.542586668220.130245909013-0.07781462970040.0932005918588-0.0876135114697-0.01673236589560.2039954620410.03841620721510.06180489476150.3919709843850.04464531089030.2744096426320.953613411212.5080319281-3.53676820327
132.753904135861.186267567640.6515120991783.715828311812.205586504416.544711633560.50120685065-0.426832333806-0.5227991448970.31191449253-0.4513894613110.04666246297330.602346883613-0.8160334400150.06719182741010.2476198598880.004221963883290.1014254763960.3191231296490.05789775782340.3553294782411.444617198-0.62967207076310.2927817626
140.4034331762340.9914084522080.2664847457891.359266927480.134328641041.583265200160.4448525208040.4554775210260.148968634751-0.0647499262041-0.2814710100630.1981230444510.3908916676570.2869424948760.115731987534-0.0217200767737-0.02711281965180.207613904250.3414665342020.06346368482820.30965191620725.874607747112.15211716525.85116292824
157.886125030810.765816291699-0.7776450780373.665718501630.2741961585023.06185538075-0.350210511168-0.8136960810491.001928122950.2899335795060.09712462368750.0282174286615-0.1029875566520.1478004940480.2873773456080.3347147097170.09282684247780.06571726773630.478842306418-0.05889913041980.44093690192422.664698699728.053532659112.6725765226
163.80446716477-0.4733569458991.818826921284.47417940523-0.6626855036361.87526283368-0.271257254326-0.8350499007110.9260341377090.3360870724950.511851825512-0.3762943339310.0242092164321-0.183682640343-0.3591856505350.6858109524790.1091122836310.3214105422320.559398233801-0.08175557356050.68457992294511.649106998124.584433322320.4478543195
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 226 through 242 )AA226 - 2421 - 17
22chain 'A' and (resid 243 through 263 )AA243 - 26318 - 31
33chain 'A' and (resid 264 through 317 )AA264 - 31732 - 85
44chain 'A' and (resid 318 through 375 )AA318 - 37586 - 145
55chain 'A' and (resid 376 through 411 )AA376 - 411146 - 181
66chain 'A' and (resid 412 through 441 )AA412 - 441182 - 211
77chain 'A' and (resid 442 through 456 )AA442 - 456212 - 226
88chain 'B' and (resid 686 through 694 )BC686 - 6941 - 9
99chain 'B' and (resid 695 through 705 )BC695 - 70510 - 20
1010chain 'C' and (resid 229 through 285 )CD229 - 2851 - 38
1111chain 'C' and (resid 286 through 330 )CD286 - 33039 - 83
1212chain 'C' and (resid 331 through 375 )CD331 - 37584 - 130
1313chain 'C' and (resid 376 through 413 )CD376 - 413131 - 168
1414chain 'C' and (resid 414 through 442 )CD414 - 442169 - 197
1515chain 'C' and (resid 443 through 458 )CD443 - 457198 - 212
1616chain 'D' and (resid 687 through 694 )DF687 - 6941 - 8

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