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- PDB-9gfi: hRAR alpha LBD-AM580 complex with staple peptide -

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Basic information

Entry
Database: PDB / ID: 9gfi
TitlehRAR alpha LBD-AM580 complex with staple peptide
Components
  • Retinoic acid receptor alpha
  • Stapled peptide-like ligand
KeywordsTRANSCRIPTION / RAR complex / staple peptide
Function / homology
Function and homology information


Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / glandular epithelial cell development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / growth plate cartilage development / protein kinase B binding / positive regulation of T-helper 2 cell differentiation ...Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / glandular epithelial cell development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / growth plate cartilage development / protein kinase B binding / positive regulation of T-helper 2 cell differentiation / prostate gland development / negative regulation of granulocyte differentiation / retinoic acid-responsive element binding / regulation of hematopoietic progenitor cell differentiation / negative regulation of cartilage development / positive regulation of interleukin-5 production / positive regulation of interleukin-13 production / retinoic acid binding / outflow tract septum morphogenesis / TGFBR3 expression / response to vitamin A / apoptotic cell clearance / Signaling by Retinoic Acid / heterocyclic compound binding / ureteric bud development / regulation of myelination / DNA-binding transcription repressor activity / limb development / positive regulation of interleukin-4 production / face development / protein kinase A binding / germ cell development / negative regulation of type II interferon production / alpha-actinin binding / cellular response to estrogen stimulus / negative regulation of tumor necrosis factor production / 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 / negative regulation of miRNA transcription / mRNA regulatory element binding translation repressor activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / hippocampus development / neural tube closure / liver development / female pregnancy / Nuclear Receptor transcription pathway / chromatin DNA binding / regulation of synaptic plasticity / mRNA transcription by RNA polymerase II / nuclear receptor activity / mRNA 5'-UTR binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription coactivator binding / multicellular organism growth / RNA polymerase II transcription regulator complex / histone deacetylase binding / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / response to estradiol / actin cytoskeleton / cellular response to lipopolysaccharide / spermatogenesis / transcription regulator complex / protein phosphorylation / response to ethanol / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / negative regulation of cell population proliferation / protein domain specific binding / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / dendrite / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / chromatin / 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 / cytoplasm / cytosol
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: 2.1 Å
AuthorsPerdriau, C. / Luton, A. / Zimmeter, K. / Neuville, M. / Saragaglia, C. / Peluso-lltis, C. / Osz, J. / Kauffmann, B. / Collie, G. / Rochel, N. ...Perdriau, C. / Luton, A. / Zimmeter, K. / Neuville, M. / Saragaglia, C. / Peluso-lltis, C. / Osz, J. / 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 1.0Feb 12, 2025Provider: repository / Type: Initial release

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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)28,3723
Polymers28,0212
Non-polymers3511
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.51, 62.06, 49.35
Angle α, β, γ (deg.)90, 105.57, 90
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 26700.170 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: 1320.693 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 20%, 0.2M NaSCN

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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: 2.1→42.12 Å / Num. obs: 14960 / % possible obs: 99.8 % / Redundancy: 2 % / Rmerge(I) obs: 0.0873 / Net I/σ(I): 17.16
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.356 / Num. unique obs: 1936

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.252 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.246 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.208
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 1497 -RANDOM
Rwork0.2233 ---
obs0.2281 14960 99.8 %-
Displacement parametersBiso mean: 52.16 Å2
Baniso -1Baniso -2Baniso -3
1-4.2203 Å20 Å20.9335 Å2
2---15.1462 Å20 Å2
3---10.926 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 119 55 2008
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081990HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.942701HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d741SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes350HARMONIC5
X-RAY DIFFRACTIONt_it1990HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion263SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1683SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion18.13
LS refinement shellResolution: 2.1→2.11 Å
RfactorNum. reflection% reflection
Rfree0.449 30 -
Rwork0.3747 --
obs0.3815 300 97.64 %

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