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- PDB-4jyi: Crystal structure of RARbeta LBD in complex with selective partia... -

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Basic information

Entry
Database: PDB / ID: 4jyi
TitleCrystal structure of RARbeta LBD in complex with selective partial agonist BMS641 [3-chloro-4-[(E)-2-(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)ethenyl]benzoic acid]
Components
  • Nuclear receptor coactivator 1
  • Retinoic acid receptor beta
KeywordsTranscription/Agonist / Ligand binding domain / Nuclear hormone receptor / Transcription-Agonist complex
Function / homology
Function and homology information


ventricular cardiac muscle cell differentiation / embryonic eye morphogenesis / growth plate cartilage development / glandular epithelial cell development / embryonic digestive tract development / striatum development / outflow tract septum morphogenesis / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway ...ventricular cardiac muscle cell differentiation / embryonic eye morphogenesis / growth plate cartilage development / glandular epithelial cell development / embryonic digestive tract development / striatum development / outflow tract septum morphogenesis / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / negative regulation of chondrocyte differentiation / embryonic hindlimb morphogenesis / neural precursor cell proliferation / regulation of myelination / Signaling by Retinoic Acid / ureteric bud development / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / hypothalamus development / male mating behavior / heterocyclic compound binding / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / negative regulation of stem cell proliferation / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / positive regulation of adipose tissue development / neurogenesis / : / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of neuron differentiation / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / hippocampus development / response to progesterone / stem cell proliferation / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / multicellular organism growth / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / sequence-specific double-stranded DNA binding / : / response to estradiol / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / Estrogen-dependent gene expression / cell differentiation / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process
Similarity search - Function
: / : / Retinoic acid receptor / Nuclear receptor coactivator 1 / 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 ...: / : / Retinoic acid receptor / Nuclear receptor coactivator 1 / 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
CITRATE ANION / Chem-JYI / Retinoic acid receptor beta / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNadendla, E.K. / Teyssier, C. / Germain, P. / Delfosse, V. / Bourguet, W.
CitationJournal: Plos One / Year: 2015
Title: An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor beta (RAR beta , NR1B2) Selective Agonist.
Authors: Nadendla, E. / Teyssier, C. / Delfosse, V. / Vivat, V. / Krishnasamy, G. / Gronemeyer, H. / Bourguet, W. / Germain, P.
History
DepositionMar 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoic acid receptor beta
B: Retinoic acid receptor beta
F: Nuclear receptor coactivator 1
G: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5977
Polymers63,5784
Non-polymers1,0193
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-30 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.520, 84.240, 109.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Retinoic acid receptor beta / RAR-beta / HBV-activated protein / Nuclear receptor subfamily 1 group B member 2 / RAR-epsilon


Mass: 30197.000 Da / Num. of mol.: 2 / Fragment: Ligand binding domain, UNP residues 176-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARB, HAP, NR1B2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P10826
#2: Protein/peptide Nuclear receptor coactivator 1 / SRC-1


Mass: 1591.880 Da / Num. of mol.: 2 / Fragment: UNP residues 686-698 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-JYI / 3-chloro-4-[(E)-2-(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)ethenyl]benzoic acid


Mass: 414.923 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H23ClO2
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLEU 414 to MET CONFLICT IN UNP ENTRY P10826

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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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 200 mM Tri Sodium Citrate pH 5.5, 25% PEG 4000, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2008 / Details: mirrors
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→48.06 Å / Num. obs: 42959 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rsym value: 0.048 / Net I/σ(I): 20.16
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.9-2.024.13.3368830.382196.1
2.02-2.154.96.1860590.2381100
2.15-2.334.910.3863400.1421100
2.33-2.554.915.555380.092199.9
2.55-2.854.922.1750370.061199.9
2.85-3.294.931.2645290.0411100
3.29-4.024.842.9838130.028199.9
4.02-5.674.750.0330180.026199.5
5.67-48.064.449.417420.025197.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.302 Å / SU ML: 0.25 / σ(F): 1.99 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 2147 5 %random
Rwork0.1965 ---
obs0.198 42949 99.23 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.935 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.3722 Å20 Å2-0 Å2
2--6.8924 Å20 Å2
3----0.5201 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 73 443 4390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044109
X-RAY DIFFRACTIONf_angle_d0.8955599
X-RAY DIFFRACTIONf_dihedral_angle_d11.5491586
X-RAY DIFFRACTIONf_chiral_restr0.103673
X-RAY DIFFRACTIONf_plane_restr0.004707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94450.3151300.27582483X-RAY DIFFRACTION92
1.9445-1.99320.25351400.24292662X-RAY DIFFRACTION99
1.9932-2.04710.3021420.23312695X-RAY DIFFRACTION100
2.0471-2.10730.24811440.22732720X-RAY DIFFRACTION100
2.1073-2.17530.27631430.22622718X-RAY DIFFRACTION100
2.1753-2.2530.26421420.21742699X-RAY DIFFRACTION100
2.253-2.34320.26721430.22642730X-RAY DIFFRACTION100
2.3432-2.44990.22791430.20992705X-RAY DIFFRACTION100
2.4499-2.5790.24891420.20912712X-RAY DIFFRACTION100
2.579-2.74060.20891440.20412729X-RAY DIFFRACTION100
2.7406-2.95210.23681450.20372751X-RAY DIFFRACTION100
2.9521-3.2490.22131450.19672753X-RAY DIFFRACTION100
3.249-3.71890.23841450.18392763X-RAY DIFFRACTION100
3.7189-4.68420.17621480.15372799X-RAY DIFFRACTION100
4.6842-39.3020.21081510.18962883X-RAY DIFFRACTION98

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