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- PDB-5k13: Crystal structure of the RAR alpha ligand-binding domain in compl... -

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Basic information

Entry
Database: PDB / ID: 5k13
TitleCrystal structure of the RAR alpha ligand-binding domain in complex with an antagonist
ComponentsRetinoic acid receptor alpha
KeywordsTRANSCRIPTION / NHR ligand-binding domain / antagonist
Function / homology
Function and homology information


Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / protein kinase B binding / negative regulation of granulocyte differentiation / growth plate cartilage development / glandular epithelial cell development ...Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / protein kinase B binding / negative regulation of granulocyte differentiation / growth plate cartilage development / glandular epithelial cell development / positive regulation of T-helper 2 cell differentiation / prostate gland development / negative regulation of cartilage development / retinoic acid-responsive element binding / regulation of hematopoietic progenitor cell differentiation / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / outflow tract septum morphogenesis / retinoic acid binding / TGFBR3 expression / response to vitamin A / limb development / apoptotic cell clearance / regulation of myelination / Signaling by Retinoic Acid / ureteric bud development / DNA-binding transcription repressor activity / protein kinase A binding / heterocyclic compound binding / positive regulation of interleukin-4 production / alpha-actinin binding / face development / germ cell development / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / cellular response to estrogen stimulus / response to retinoic acid / retinoic acid receptor signaling pathway / cellular response to retinoic acid / positive regulation of cell cycle / response to cytokine / positive regulation of neuron differentiation / mRNA regulatory element binding translation repressor activity / negative regulation of miRNA transcription / liver development / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / female pregnancy / neural tube closure / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / transcription coactivator binding / multicellular organism growth / regulation of synaptic plasticity / Nuclear Receptor transcription pathway / chromatin DNA binding / mRNA 5'-UTR binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / nuclear receptor activity / sequence-specific double-stranded DNA binding / response to estradiol / actin cytoskeleton / cellular response to lipopolysaccharide / spermatogenesis / transcription regulator complex / response to ethanol / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein phosphorylation / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / dendrite / chromatin binding / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Retinoic acid receptor / Retinoid X Receptor / Retinoid X Receptor / 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. ...: / : / Retinoic acid receptor / Retinoid X Receptor / Retinoid X Receptor / 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-6Q7 / Retinoic acid receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWang, Y. / Stout, S.L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Identification of potent and selective retinoic acid receptor gamma (RAR gamma ) antagonists for the treatment of osteoarthritis pain using structure based drug design.
Authors: Hughes, N.E. / Bleisch, T.J. / Jones, S.A. / Richardson, T.I. / Doti, R.A. / Wang, Y. / Stout, S.L. / Durst, G.L. / Chambers, M.G. / Oskins, J.L. / Lin, C. / Adams, L.A. / Page, T.J. / Barr, ...Authors: Hughes, N.E. / Bleisch, T.J. / Jones, S.A. / Richardson, T.I. / Doti, R.A. / Wang, Y. / Stout, S.L. / Durst, G.L. / Chambers, M.G. / Oskins, J.L. / Lin, C. / Adams, L.A. / Page, T.J. / Barr, R.J. / Zink, R.W. / Osborne, H. / Montrose-Rafizadeh, C. / Norman, B.H.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoic acid receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1642
Polymers27,6891
Non-polymers4751
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.496, 62.541, 49.347
Angle α, β, γ (deg.)90.000, 106.050, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-713-

HOH

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Components

#1: Protein Retinoic acid receptor alpha / RAR-alpha / Nuclear receptor subfamily 1 group B member 1


Mass: 27689.123 Da / Num. of mol.: 1 / Fragment: UNP residues 176-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARA, NR1B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10276
#2: Chemical ChemComp-6Q7 / 4-{5-(3-tert-butylphenyl)-1-[4-(methylsulfonyl)phenyl]-1H-pyrazol-3-yl}benzoic acid


Mass: 474.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H26N2O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 10-20% PEG 3350, 0.2M di-ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97983 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97983 Å / Relative weight: 1
ReflectionResolution: 1.715→23.932 Å / Num. obs: 26830 / % possible obs: 96.6 % / Redundancy: 5 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.105 / Rsym value: 0.085 / Net I/av σ(I): 5.13 / Net I/σ(I): 11 / Num. measured all: 134739
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.715-1.814.50.4361.2191.4
1.81-1.925.10.3650.9196.7
1.92-2.055.20.1773.1197.2
2.05-2.215.20.1154.4197.5
2.21-2.4350.1283.1197.4
2.43-2.715.20.0758.4198.3
2.71-3.135.10.0698.8198.5
3.13-3.835.10.0658.9199
3.83-5.4250.05610.6198.7
5.42-23.9324.70.0589.8191.8

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Processing

Software
NameVersionClassification
SCALA3.2.5data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DKF

1dkf


Resolution: 1.85→23.93 Å / Cor.coef. Fo:Fc: 0.9377 / Cor.coef. Fo:Fc free: 0.9162 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.127
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 1106 5.14 %RANDOM
Rwork0.1945 ---
obs0.196 21510 97 %-
Displacement parametersBiso max: 120.52 Å2 / Biso mean: 24.85 Å2 / Biso min: 3.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.186 Å20 Å21.0987 Å2
2---2.1835 Å20 Å2
3---0.9975 Å2
Refine analyzeLuzzati coordinate error obs: 0.248 Å
Refinement stepCycle: final / Resolution: 1.85→23.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 34 153 2011
Biso mean--15.74 33.44 -
Num. residues----235
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d692SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes288HARMONIC5
X-RAY DIFFRACTIONt_it1917HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion267SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2403SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1917HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2612HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion15.32
LS refinement shellResolution: 1.85→1.94 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3772 128 4.62 %
Rwork0.3364 2643 -
all0.3383 2771 -
obs--94.4 %

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