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

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Basic information

Entry
Database: PDB / ID: 7yxn
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
Function / homology
Function and homology information


bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / animal organ regeneration / response to glucose / nuclear retinoid X receptor binding / Notch signaling pathway / cholesterol metabolic process / circadian regulation of gene expression ...bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / animal organ regeneration / response to glucose / nuclear retinoid X receptor binding / Notch signaling pathway / cholesterol metabolic process / circadian regulation of gene expression / negative regulation of DNA-binding transcription factor activity / positive regulation of insulin secretion / response to organic cyclic compound / Nuclear Receptor transcription pathway / circadian rhythm / transcription corepressor activity / response to ethanol / protein domain specific binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / protein-containing complex binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / 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
Similarity search - Domain/homology
DEXAMETHASONE / FORMIC ACID / 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: 2.46 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
CitationJournal: 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.
History
DepositionFeb 16, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,04910
Polymers60,0804
Non-polymers9696
Water905
1
A: Ancestral Glucocorticoid Receptor2
R: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5245
Polymers30,0402
Non-polymers4853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-12 kcal/mol
Surface area12200 Å2
MethodPISA
2
C: Ancestral Glucocorticoid Receptor2
S: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5245
Polymers30,0402
Non-polymers4853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-9 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.479, 109.479, 137.781
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13R
23S

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYARGARGAA527 - 7041 - 178
21GLYGLYARGARGCB527 - 7041 - 178
12ASNASNPHEPHEAA711 - 774185 - 248
22ASNASNPHEPHECB711 - 774185 - 248
13ARGARGSERSERRC17 - 271 - 11
23ARGARGSERSERSD17 - 271 - 11

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Ancestral Glucocorticoid Receptor2


Mass: 28835.523 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15466
#3: Chemical ChemComp-DEX / DEXAMETHASONE / 9A-FLUORO-16BETA-METHYLPREDNISOLONE / Dexamethasone


Mass: 392.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29FO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: 4 Å3/Da / Density % sol: 69.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M PIPES, pH 7.0, 0.1 M ammonium acetate, 2.5 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.46→94.81 Å / Num. obs: 33009 / % possible obs: 96.8 % / Redundancy: 2.9 % / CC1/2: 0.994 / Rpim(I) all: 0.051 / Rrim(I) all: 0.074 / Net I/σ(I): 7.4
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3799 / CC1/2: 0.317 / Rpim(I) all: 0.725 / % possible all: 98.5

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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: 2.46→94.81 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.749 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1692 5.1 %RANDOM
Rwork0.2162 ---
obs0.2177 31272 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 179.89 Å2 / Biso mean: 68.274 Å2 / Biso min: 29.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å2-0 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 2.46→94.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 68 5 4188
Biso mean--46.6 52 -
Num. residues----509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124275
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6255784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2815503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31422.438201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.40415786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4141522
X-RAY DIFFRACTIONr_chiral_restr0.130.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023096
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A57640.1
12C57640.1
21A19190.09
22C19190.09
31R2640.15
32S2640.15
LS refinement shellResolution: 2.46→2.52 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.311 123 -
Rwork0.362 2385 -
obs--98.66 %

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