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- PDB-7yxc: Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP... -

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Basic information

Entry
Database: PDB / ID: 7yxc
TitleCrystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment
Components
  • Ancestral Glucocorticoid Receptor2
  • SHP NR Box 1 Peptide
KeywordsNUCLEAR PROTEIN / Nuclear Receptor / Transcription Factor / Dexamethasone / Nuclear receptor subfamily 0 group B member 2
Function / homology
Function and homology information


peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / bile acid and bile salt transport / animal organ regeneration / nuclear retinoid X receptor binding / transcription regulator inhibitor activity / response to glucose / Notch signaling pathway / cholesterol metabolic process / negative regulation of DNA-binding transcription factor activity ...peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / bile acid and bile salt transport / animal organ regeneration / nuclear retinoid X receptor binding / transcription regulator inhibitor activity / response to glucose / Notch signaling pathway / cholesterol metabolic process / negative regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / : / positive regulation of insulin secretion / Nuclear Receptor transcription pathway / circadian rhythm / transcription corepressor activity / response to ethanol / protein domain specific binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / positive regulation of gene expression / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / 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 ...Nuclear receptor subfamily 0 group B member 1/2 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBONATE ION / DEXAMETHASONE / Ancestral Glucocorticoid Receptor2 / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesunidentified (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJimenez-Panizo, A. / Estebanez-Perpina, E. / Fuentes-Prior, P.
Funding support Spain, 4items
OrganizationGrant numberCountry
Other governmentBFU-Retos2017-86906-R Spain
Other governmentSAF2017-71878-REDT Spain
Other governmentSAF2015-71878-REDT Spain
Other governmentRTI2018-101500-B-I00 Spain
Citation
Journal: Nucleic Acids Res. / Year: 2022
Title: The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities.
Authors: Jimenez-Panizo, A. / Alegre-Marti, A. / Tettey, T.T. / Fettweis, G. / Abella, M. / Anton, R. / Johnson, T.A. / Kim, S. / Schiltz, R.L. / Nunez-Barrios, I. / Font-Diaz, J. / Caelles, C. / ...Authors: Jimenez-Panizo, A. / Alegre-Marti, A. / Tettey, T.T. / Fettweis, G. / Abella, M. / Anton, R. / Johnson, T.A. / Kim, S. / Schiltz, R.L. / Nunez-Barrios, I. / Font-Diaz, J. / Caelles, C. / Valledor, A.F. / Perez, P. / Rojas, A.M. / Fernandez-Recio, J. / Presman, D.M. / Hager, G.L. / Fuentes-Prior, P. / Estebanez-Perpina, E.
#1: Journal: Biorxiv / Year: 2021
Title: The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities
Authors: Jimenez-Panizo, A. / Alegre-Marti, A. / Fettweis, G. / Abella, M. / Anton, R. / Tettey, T. / Schiltz, L.R. / Johnson, T.A. / Nunez-Barrios, I. / Font-Diaz, J. / Caelles, C. / Valledor, A.F. ...Authors: Jimenez-Panizo, A. / Alegre-Marti, A. / Fettweis, G. / Abella, M. / Anton, R. / Tettey, T. / Schiltz, L.R. / Johnson, T.A. / Nunez-Barrios, I. / Font-Diaz, J. / Caelles, C. / Valledor, A.F. / Perez, P. / Rojas, A.M. / Fernandez-Recio, J. / Presman, D.M. / Hager, G.L. / Fuentes-Prior, P. / Estebanez-Perpina, E.
History
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 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

Downloads & links

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Assembly

Deposited unit
A: Ancestral Glucocorticoid Receptor2
R: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5616
Polymers29,8542
Non-polymers7074
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-4 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.605, 52.435, 69.600
Angle α, β, γ (deg.)90.000, 116.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1123-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AR

#1: Protein Ancestral Glucocorticoid Receptor2


Mass: 28649.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X8XLE9
#2: Protein/peptide SHP NR Box 1 Peptide / Orphan nuclear receptor SHP / Small heterodimer partner / Nuclear receptor subfamily 0 group B member 2


Mass: 1204.440 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR0B2, SHP / Production host: synthetic construct (others) / References: UniProt: Q15466

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Non-polymers , 4 types, 28 molecules

#3: Chemical ChemComp-DEX / DEXAMETHASONE / 9A-FLUORO-16BETA-METHYLPREDNISOLONE


Mass: 392.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29FO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 85 mM sodium cacodylate trihydrate, pH 6.5, 0.17 M sodium acetate trihydrate, 25.5% (w/v) PEG8000, 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.25→43.42 Å / Num. obs: 12530 / % possible obs: 93.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 44.7 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.039 / Rrim(I) all: 0.069 / Net I/σ(I): 11.1
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 907 / CC1/2: 0.654 / Rpim(I) all: 0.439 / Rrim(I) all: 0.697 / % possible all: 75.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UFS

5ufs


Resolution: 2.25→43.42 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.412 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 510 4.1 %RANDOM
Rwork0.1929 ---
obs0.195 12018 93.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.98 Å2 / Biso mean: 54.908 Å2 / Biso min: 25.09 Å2
Baniso -1Baniso -2Baniso -3
1--22.48 Å2-0 Å213.9 Å2
2---9.15 Å20 Å2
3---31.63 Å2
Refinement stepCycle: final / Resolution: 2.25→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 49 24 2146
Biso mean--49.61 45.47 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122166
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6252927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0555253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83822.549102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70915396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.1311511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021568
LS refinement shellResolution: 2.25→2.309 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 30 -
Rwork0.263 701 -
all-731 -
obs--73.91 %

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