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- PDB-5mj5: Crystal structure of the Retinoid X Receptor alpha in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5mj5
TitleCrystal structure of the Retinoid X Receptor alpha in complex with synthetichonokiol derivative 3 and a fragment of the TIF2 co-activator.
Components
  • LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP-SER
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / RXR TIF2 honokiol
Function / homology
Function and homology information


DNA binding domain binding / 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 / LBD domain binding / Carnitine metabolism ...DNA binding domain binding / 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 / LBD domain binding / Carnitine metabolism / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Synthesis of bile acids and bile salts / hormone-mediated signaling pathway / peroxisome proliferator activated 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / transcription coregulator binding / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / Heme signaling / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / receptor complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / chromatin / 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 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / : / Retinoid X receptor/HNF4 / Retinoid X Receptor / Retinoid X Receptor / 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 / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Ligand-binding domain of nuclear hormone receptor / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7O0 / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsAndrei, S.A. / Brunsveld, L. / Scheepstra, M. / 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
DepositionNov 30, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
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

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
B: LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5813
Polymers27,2512
Non-polymers3301
Water2,288127
1
A: Retinoic acid receptor RXR-alpha
B: LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP-SER
hetero molecules

A: Retinoic acid receptor RXR-alpha
B: LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1626
Polymers54,5014
Non-polymers6612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)68.159, 68.159, 109.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-667-

HOH

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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.: 1
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 LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP-SER


Mass: 1579.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-7O0 / (~{E})-3-[4-oxidanyl-3-[3-(phenylmethyl)phenyl]phenyl]prop-2-enoic acid


Mass: 330.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M PIPES, pH 7.0, 0.1 M 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: 1.9→68.16 Å / Num. obs: 21110 / % possible obs: 99.9 % / Redundancy: 20.9 % / Biso Wilson estimate: 36.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.9-1.949.81.0640.51199.2
9.11-68.1617.90.0510.999199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.45 Å57.9 Å
Translation6.45 Å57.9 Å

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
PHASER2.6.0phasing
PHENIX1.10.1-2155refinement
PDB_EXTRACT3.2data extraction
iMOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EC9

5ec9


Resolution: 1.9→57.897 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.82
RfactorNum. reflection% reflection
Rfree0.2428 418 1.99 %
Rwork0.1966 --
obs0.1975 21049 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.05 Å2 / Biso mean: 46.1987 Å2 / Biso min: 23 Å2
Refinement stepCycle: final / Resolution: 1.9→57.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 43 127 1954
Biso mean--35.54 45.14 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011909
X-RAY DIFFRACTIONf_angle_d0.3612585
X-RAY DIFFRACTIONf_chiral_restr0.034290
X-RAY DIFFRACTIONf_plane_restr0.002355
X-RAY DIFFRACTIONf_dihedral_angle_d12.8861184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-2.1750.30911350.233267066841
2.175-2.74020.24231230.227668326955
2.7402-57.9240.23291600.181370937253
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)
18.98625.71645.10958.49065.49667.95810.18740.1589-0.48830.61920.192-1.58220.19490.9947-0.3930.3516-0.02-0.05630.61240.09320.371218.2834-11.21563.8361
22.99110.1960.17193.92150.64093.43870.0627-0.1939-0.49670.5196-0.0184-0.12790.14830.4707-0.08650.26390.0417-0.07450.34020.06680.31458.4441-15.33756.8564
37.28861.06321.15783.6348-0.94522.04920.0411.3374-0.3921-0.76840.08120.22440.0480.4519-0.25170.43690.0935-0.08280.5728-0.21210.48084.9861-20.9455-13.8283
43.24351.01061.1344.94890.91434.2058-0.17690.4851-0.1084-0.33090.0063-0.1675-0.18110.51250.18010.2362-0.0016-0.01060.45340.01150.23467.0319-8.052-6.7604
54.20651.72750.3015.7694-1.94352.63940.01890.02980.31420.712-0.0862-0.3576-0.59960.47620.06110.4047-0.1137-0.12880.38220.00080.322210.78272.36056.7543
63.43890.12290.98336.8228-0.51163.49580.00440.0293-0.4411-0.11550.03350.30890.01760.0501-0.05320.14040.0164-0.03180.29270.00470.228-0.8239-10.0162-1.7173
73.35841.59655.41456.09541.78198.84620.5587-0.3379-1.25380.07680.04260.72551.2554-0.6221-0.4960.4386-0.0281-0.05160.47590.13320.808-1.4202-26.64756.6135
89.93013.3573-3.73762.0761-3.22077.83120.0044-1.1812-1.41361.593-0.124-0.53850.0212-0.31860.14960.68870.0839-0.00080.54420.15120.57798.4791-21.939919.1382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 229 through 263 )A229 - 263
2X-RAY DIFFRACTION2chain 'A' and (resid 264 through 318 )A264 - 318
3X-RAY DIFFRACTION3chain 'A' and (resid 319 through 340 )A319 - 340
4X-RAY DIFFRACTION4chain 'A' and (resid 341 through 375 )A341 - 375
5X-RAY DIFFRACTION5chain 'A' and (resid 376 through 413 )A376 - 413
6X-RAY DIFFRACTION6chain 'A' and (resid 414 through 441 )A414 - 441
7X-RAY DIFFRACTION7chain 'A' and (resid 442 through 456 )A442 - 456
8X-RAY DIFFRACTION8chain 'B' and (resid 472 through 481 )B472 - 481

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