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- PDB-9gfe: hRAR LBD protein in complex with AM580 agonist ligand and a stapl... -

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Basic information

Entry
Database: PDB / ID: 9gfe
TitlehRAR LBD protein in complex with AM580 agonist ligand and a stapled peptide
Components
  • Retinoic acid receptor alpha
  • Stapled peptide-like ligand
KeywordsTRANSCRIPTION / hRAR LBD protein / complex / stapled peptide
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 / 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 ...: / : / Retinoic acid 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
Similarity search - Domain/homology
Chem-EQN / Retinoic acid receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.583 Å
AuthorsPerdriau, C. / Luton, A. / Zimmeter, K. / Neuville, M. / Saragaglia, C. / Peluso-lltis, C. / Kauffmann, B. / Collie, G. / Rochel, N. / Guichard, G. / Pasco, M.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE07-0010 France
Agence Nationale de la Recherche (ANR)ANR-17-CE07-0020 France
Agence Nationale de la Recherche (ANR)ANR-20-CE18-0038 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Guanidinium-Stapled Helical Peptides for Targeting Protein-Protein Interactions.
Authors: Perdriau, C. / Luton, A. / Zimmeter, K. / Neuville, M. / Saragaglia, C. / Peluso-Iltis, C. / Osz, J. / Kauffmann, B. / Collie, G.W. / Rochel, N. / Guichard, G. / Pasco, M.
History
DepositionAug 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid receptor alpha
B: Stapled peptide-like ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1373
Polymers27,7862
Non-polymers3511
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.66, 62.34, 49.47
Angle α, β, γ (deg.)90, 105.3, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-660-

HOH

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Components

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


Mass: 26587.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARA, NR1B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P10276
#2: Protein/peptide Stapled peptide-like ligand


Mass: 1198.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EQN / 4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid


Mass: 351.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: PEG 3350 20%, 0.2M Lithium Acetate, 0.05M NH4 Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.58→37.6 Å / Num. obs: 33762 / % possible obs: 96.31 % / Redundancy: 2 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 17.5
Reflection shellResolution: 1.58→1.68 Å / Rmerge(I) obs: 0.5313 / Num. unique obs: 5222

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.583→28.17 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1996 -RANDOM
Rwork0.2042 ---
obs0.2057 33762 96.3 %-
Displacement parametersBiso mean: 30.79 Å2
Baniso -1Baniso -2Baniso -3
1-4.3032 Å20 Å21.6386 Å2
2---7.4334 Å20 Å2
3---3.1302 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.583→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 112 162 2106
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012017HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.022745HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d759SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes358HARMONIC5
X-RAY DIFFRACTIONt_it2017HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion277SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2036SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion15.18
LS refinement shellResolution: 1.583→1.6 Å
RfactorNum. reflection% reflection
Rfree0.4008 40 -
Rwork0.366 --
obs--67.85 %

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