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- PDB-5mk4: Crystal structure of the Retinoid X Receptor alpha in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5mk4
TitleCrystal structure of the Retinoid X Receptor alpha in complex with synthetic honokiol derivative 7 and a fragment of the TIF2 co-activator.
Components
  • Nuclear receptor coactivator 2
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / RXR TIF2 Honokiol
Function / homology
Function and homology information


retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / 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 shuttle / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway ...retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / 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 shuttle / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / DNA binding domain binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / positive regulation of bone mineralization / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / transcription regulator inhibitor activity / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / hormone-mediated signaling pathway / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear receptor activity / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / : / nervous system development / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / receptor complex / transcription cis-regulatory region binding / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / 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 / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / 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, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily ...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 / 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 / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-I5W / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsAndrei, S.A. / Scheepstra, M. / Brunsveld, L. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWOECHO 711011017 Netherlands
CitationJournal: ACS Chem Neurosci / Year: 2017
Title: Ligand Dependent Switch from RXR Homo- to RXR-NURR1 Heterodimerization.
Authors: Scheepstra, M. / Andrei, S.A. / de Vries, R.M.J.M. / Meijer, F.A. / Ma, J.N. / Burstein, E.S. / Olsson, R. / Ottmann, C. / Milroy, L.G. / Brunsveld, L.
History
DepositionDec 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 17, 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
C: Retinoic acid receptor RXR-alpha
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8858
Polymers54,1534
Non-polymers7324
Water8,575476
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.699, 74.140, 99.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 25670.793 Da / Num. of mol.: 2 / Fragment: UNP residues 229-457
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 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1405.710 Da / Num. of mol.: 2 / Fragment: UNP residues 686-696 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-I5W / (~{E})-3-[3-(2-methyl-5-phenyl-phenyl)-4-oxidanyl-phenyl]prop-2-enoic acid


Mass: 330.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H18O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M PIPES, pH 7.0, 0.1M NaCl, 22% PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0331 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2→99.21 Å / Num. obs: 36452 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 27.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.038 / Rrim(I) all: 0.129 / Net I/σ(I): 13.1 / Num. measured all: 399571 / Scaling rejects: 251
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.057.30.8971908026230.6550.3440.9652.299.1
8.94-99.219.60.146784880.9950.0320.10528.499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.19 Å59.39 Å
Translation5.19 Å59.39 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.29data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
MOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EC9

5ec9


Resolution: 2→59.389 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 1823 5.01 %
Rwork0.1707 34557 -
obs0.1737 36380 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.94 Å2 / Biso mean: 33.7591 Å2 / Biso min: 12.07 Å2
Refinement stepCycle: final / Resolution: 2→59.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 86 476 4127
Biso mean--26.34 42.4 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093869
X-RAY DIFFRACTIONf_angle_d1.1695244
X-RAY DIFFRACTIONf_chiral_restr0.068585
X-RAY DIFFRACTIONf_plane_restr0.009679
X-RAY DIFFRACTIONf_dihedral_angle_d11.3884026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.05410.29211300.22222584271499
2.0541-2.11450.2491120.201926652777100
2.1145-2.18280.23721180.192526362754100
2.1828-2.26080.35431320.24826232755100
2.2608-2.35130.28011410.192126212762100
2.3513-2.45830.24081390.157426602799100
2.4583-2.5880.23031290.17226202749100
2.588-2.75010.21171400.162726732813100
2.7501-2.96240.23681300.175126492779100
2.9624-3.26050.24641620.17626492811100
3.2605-3.73230.22031420.154126792821100
3.7323-4.7020.19491900.136626732863100
4.702-59.41470.211580.171828252983100
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)
11.68591.74970.11016.97741.47081.12180.5179-0.045-0.84910.31-0.2284-0.03210.8116-0.1985-0.26720.4746-0.00940.06710.1973-0.03030.55828.3633-16.5779-11.688
22.51590.06810.37351.69720.40493.32840.02980.0429-0.40630.05540.00770.09490.33540.0972-0.05930.19790.04090.00440.1344-0.03580.202733.6558-8.8806-12.5454
33.55361.21.23933.52961.31782.65030.1746-0.5058-0.27460.4775-0.2070.21050.3035-0.26030.02290.2622-0.01830.02620.18070.02880.187926.3321-4.1873-1.4719
44.74842.2683-1.53023.8149-2.22115.6114-0.03580.4476-0.6498-0.29390.05290.4830.6704-0.4234-0.04320.2565-0.0169-0.03930.2045-0.12560.523315.69-11.0868-18.3671
58.35314.27351.28375.02870.94321.39520.0783-0.14470.08870.2101-0.07490.3660.10380.0368-0.00430.17030.01230.00730.11940.00290.131927.11141.9675-9.7098
66.53954.4653.89485.26376.33988.4612-0.38860.5864-0.1205-0.49290.4553-0.3563-0.42060.7898-0.11670.2486-0.01860.02250.2661-0.03790.218944.28430.8941-16.2913
76.20990.54360.54315.00840.17318.3138-0.0113-0.20560.2167-0.57690.0044-0.2658-0.37050.0770.0040.28020.09950.03560.2801-0.06350.205541.7521-8.6032-26.4944
86.97652.9531-0.72764.3958-0.54640.6347-0.28670.7875-0.016-0.38440.5980.89030.2884-0.6939-0.35240.2086-0.0061-0.02790.4511-0.10940.4320.395412.6944-14.4584
92.46210.2043-0.17213.05260.26132.5693-0.02120.18-0.0928-0.1117-0.09740.3646-0.1569-0.37820.07390.11550.0235-0.02120.1835-0.05080.18738.721617.3566-12.2982
103.80111.0397-0.93482.4283-0.43752.5752-0.05540.5695-0.2845-0.4250.02940.22670.0949-0.2848-0.00830.20670.0005-0.04460.2802-0.05720.20212.899410.3457-24.0275
113.70962.08541.60213.9391.2062.44820.1427-0.4932-0.94780.54620.00530.5660.4267-0.6278-0.07350.1988-0.09840.04480.2666-0.02670.56425.38-0.5274-7.3814
124.72164.0261-0.27077.78610.43591.9709-0.1310.2843-0.3853-0.35880.158-0.2747-0.05980.059-0.05480.1254-0.0088-0.02670.1715-0.00880.138819.173410.9026-15.7232
139.12976.422-7.11314.5252-5.01695.5830.0633-0.27320.1764-0.0152-0.2183-0.1926-0.30510.60550.25590.2648-0.0245-0.02130.2866-0.04330.229918.075727.3948-8.0677
148.0965-3.56531.59147.7932-0.45367.6644-0.0621-0.86640.15030.4184-0.1317-0.153-0.0102-0.26380.18480.19210.0110.02680.2344-0.06110.18358.162124.80061.5881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 229 through 262 )A229 - 262
2X-RAY DIFFRACTION2chain 'A' and (resid 263 through 330 )A263 - 330
3X-RAY DIFFRACTION3chain 'A' and (resid 331 through 375 )A331 - 375
4X-RAY DIFFRACTION4chain 'A' and (resid 376 through 413 )A376 - 413
5X-RAY DIFFRACTION5chain 'A' and (resid 414 through 441 )A414 - 441
6X-RAY DIFFRACTION6chain 'A' and (resid 442 through 457 )A442 - 457
7X-RAY DIFFRACTION7chain 'B' and (resid 471 through 480 )B471 - 480
8X-RAY DIFFRACTION8chain 'C' and (resid 229 through 262 )C229 - 262
9X-RAY DIFFRACTION9chain 'C' and (resid 263 through 330 )C263 - 330
10X-RAY DIFFRACTION10chain 'C' and (resid 331 through 375 )C331 - 375
11X-RAY DIFFRACTION11chain 'C' and (resid 376 through 413 )C376 - 413
12X-RAY DIFFRACTION12chain 'C' and (resid 414 through 442 )C414 - 442
13X-RAY DIFFRACTION13chain 'C' and (resid 443 through 457 )C443 - 457
14X-RAY DIFFRACTION14chain 'D' and (resid 471 through 481 )D471 - 481

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