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

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Basic information

Entry
Database: PDB / ID: 7yxo
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


peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / bile acid and bile salt transport / animal organ regeneration / response to glucose / : / nuclear retinoid X receptor binding / cholesterol metabolic process / transcription regulator inhibitor activity / Notch signaling pathway ...peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / bile acid and bile salt transport / animal organ regeneration / response to glucose / : / nuclear retinoid X receptor binding / cholesterol metabolic process / transcription regulator inhibitor activity / Notch signaling pathway / circadian regulation of gene expression / circadian rhythm / positive regulation of insulin secretion / Nuclear Receptor transcription pathway / 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 / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / 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
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: 2.99 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
B: SHP NR Box 1 Peptide
C: Ancestral Glucocorticoid Receptor2
D: SHP NR Box 1 Peptide
E: Ancestral Glucocorticoid Receptor2
F: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,25714
Polymers89,5616
Non-polymers2,6958
Water1448
1
A: Ancestral Glucocorticoid Receptor2
B: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9575
Polymers29,8542
Non-polymers1,1033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-22 kcal/mol
Surface area12080 Å2
MethodPISA
2
C: Ancestral Glucocorticoid Receptor2
D: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0536
Polymers29,8542
Non-polymers1,1994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-33 kcal/mol
Surface area12460 Å2
MethodPISA
3
E: Ancestral Glucocorticoid Receptor2
F: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2463
Polymers29,8542
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-13 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.200, 180.200, 169.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-1003-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISAA530 - 7752 - 247
21HISHISCC530 - 7752 - 247
12LEULEUAA530 - 7732 - 245
22LEULEUEE530 - 7732 - 245
13LEULEUCC530 - 7732 - 245
23LEULEUEE530 - 7732 - 245

NCS ensembles :
ID
1
2
3

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ACEBDF

#1: Protein Ancestral Glucocorticoid Receptor2


Mass: 28649.363 Da / Num. of mol.: 3
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.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15466

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Non-polymers , 4 types, 16 molecules

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


Mass: 392.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H29FO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.87 Å3/Da / Density % sol: 68.19 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate

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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 7, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.748
11L, -K, H20.124
11-H, L, K30.128
ReflectionResolution: 2.99→90.1 Å / Num. obs: 23704 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 73.5 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.149 / Rrim(I) all: 0.307 / Net I/σ(I): 6.6
Reflection shellResolution: 2.99→3.18 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4229 / CC1/2: 0.386 / Rpim(I) all: 0.815 / % possible all: 100

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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: 2.99→90.1 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.825 / SU B: 20.234 / SU ML: 0.378 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 1194 5 %RANDOM
Rwork0.2417 ---
obs0.2437 22492 83.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.94 Å2 / Biso mean: 67.754 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--15 Å2-0 Å2-0 Å2
2---15 Å2-0 Å2
3---29.99 Å2
Refinement stepCycle: final / Resolution: 2.99→90.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5918 0 183 8 6109
Biso mean--55.4 33.47 -
Num. residues----732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126233
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6248454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5655719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05122.456285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.057151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5881530
X-RAY DIFFRACTIONr_chiral_restr0.1230.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024399
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73960.17
12C73960.17
21A69460.19
22E69460.19
31C69320.19
32E69320.19
LS refinement shellResolution: 2.992→3.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20

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