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

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Basic information

Entry
Database: PDB / ID: 5mmw
TitleCrystal structure of the Retinoid X Receptor alpha in complex with synthetic honokiol derivative 6 and a fragment of the TIF2 co-activator.
Components
  • LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / RXR TIF2 honokiol transcription
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 shuttle / TGFBR3 expression / retinoic acid 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 / Carnitine shuttle / TGFBR3 expression / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / DNA binding domain binding / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / retinoic acid receptor signaling pathway / positive regulation of bone mineralization / response to retinoic acid / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / 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 / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 / Ligand-binding domain of nuclear hormone receptor / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-SJZ / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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
DepositionDec 12, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,0243
Polymers26,6942
Non-polymers3301
Water1448
1
A: Retinoic acid receptor RXR-alpha
B: LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)54,0496
Polymers53,3884
Non-polymers6612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)67.489, 67.489, 108.639
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-606-

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-ILE-LEU-HIS-ARG-LEU-LEU-GLN


Mass: 1023.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SJZ / (~{E})-3-[3-(2-methyl-3-phenyl-phenyl)-4-oxidanyl-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.: 8 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.0, 0.1M PIPES, 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: 2.7→67.49 Å / Num. obs: 7394 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 56.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.035 / Rrim(I) all: 0.159 / Net I/σ(I): 14 / Num. measured all: 154514 / Scaling rejects: 31
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.7-2.8321.20.9290.8621100
8.96-67.49170.0740.999199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.24 Å57.33 Å
Translation6.24 Å57.33 Å

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
iMOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ec9

5ec9


Resolution: 2.7→47.722 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.11
RfactorNum. reflection% reflection
Rfree0.2529 738 10.04 %
Rwork0.1997 --
obs0.2048 7351 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 191.77 Å2 / Biso mean: 62.2629 Å2 / Biso min: 27.27 Å2
Refinement stepCycle: final / Resolution: 2.7→47.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 42 8 1794
Biso mean--59.23 46.46 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011804
X-RAY DIFFRACTIONf_angle_d0.3832437
X-RAY DIFFRACTIONf_chiral_restr0.033278
X-RAY DIFFRACTIONf_plane_restr0.002310
X-RAY DIFFRACTIONf_dihedral_angle_d15.5441095
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7002-2.90870.31551480.256412741422
2.9087-3.20130.25631520.235112891441
3.2013-3.66440.26241340.224313031437
3.6644-4.61620.21161350.171313341469
4.6162-47.72920.2621690.187614131582
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)
15.97181.90020.01926.0516-1.13362.6459-0.24390.1731-0.7730.20280.3203-0.95950.05870.90050.01240.40720.0362-0.12610.62840.04190.406313.5043-16.25244.2713
24.5554-0.38440.36664.915-0.4223.7328-0.03750.212-0.2556-0.0824-0.0296-0.1111-0.12560.54590.03740.36180.0108-0.02970.52040.01010.29946.8319-11.1876-0.4864
34.762-0.28090.37125.6418-0.42224.4139-0.09670.16270.18690.27230.1235-0.2226-0.4590.4667-0.08470.37430.0263-0.00630.44770.04620.27936.5771-2.62221.0512
43.80960.72755.49718.5311-1.68759.80640.5048-0.0901-1.97280.4769-0.17171.17341.5378-0.1702-0.23530.53960.05640.10010.5270.04170.9295-1.5482-25.93916.8828
58.75792.2872-1.79417.03391.32922.8572-0.0935-1.1319-0.71021.5226-0.431-0.75280.0834-0.14220.56871.23630.04680.00310.7010.18590.4668.2005-21.053818.552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 229 through 285 )A229 - 285
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 385 )A286 - 385
3X-RAY DIFFRACTION3chain 'A' and (resid 386 through 441 )A386 - 441
4X-RAY DIFFRACTION4chain 'A' and (resid 442 through 457 )A442 - 457
5X-RAY DIFFRACTION5chain 'B' and (resid 473 through 480 )B473 - 480

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