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

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Basic information

Entry
Database: PDB / ID: 7yxd
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


transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / bile acid and bile salt transport / 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 ...transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / bile acid and bile salt transport / 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 / positive regulation of insulin secretion / negative regulation of DNA-binding transcription factor activity / response to organic cyclic compound / Nuclear Receptor transcription pathway / circadian rhythm / transcription corepressor activity / response to ethanol / protein domain specific binding / intracellular membrane-bounded organelle / negative regulation of gene expression / negative regulation of DNA-templated transcription / protein-containing complex binding / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / 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 / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Ligand-binding domain of nuclear hormone receptor
Similarity search - Domain/homology
DEXAMETHASONE / : / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesunidentified (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 ...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: SHP NR Box 1 Peptide
D: Ancestral Glucocorticoid Receptor2
F: SHP NR Box 1 Peptide
H: Ancestral Glucocorticoid Receptor2
J: SHP NR Box 1 Peptide
L: Ancestral Glucocorticoid Receptor2
N: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,35613
Polymers119,7648
Non-polymers1,5935
Water1448
1
A: Ancestral Glucocorticoid Receptor2
C: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3333
Polymers29,9412
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-12 kcal/mol
Surface area12050 Å2
MethodPISA
2
D: Ancestral Glucocorticoid Receptor2
F: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3333
Polymers29,9412
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-13 kcal/mol
Surface area11680 Å2
MethodPISA
3
H: Ancestral Glucocorticoid Receptor2
J: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3564
Polymers29,9412
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-19 kcal/mol
Surface area11970 Å2
MethodPISA
4
L: Ancestral Glucocorticoid Receptor2
N: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3333
Polymers29,9412
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-10 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.599, 107.599, 135.641
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22H
13A
23L
14A
24D
15A
25H
16A
26L
17C
27F
18C
28N
19D
29H
110D
210L
111D
211H
112D
212L
113F
213N
114H
214L
115H
215L

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLYSLYSAA530 - 7032 - 175
21PROPROLYSLYSDC530 - 7032 - 175
12PHEPHEARGARGAA529 - 7041 - 176
22PHEPHEARGARGHE529 - 7041 - 176
13PHEPHEARGARGAA529 - 7041 - 176
23PHEPHEARGARGLG529 - 7041 - 176
14TRPTRPPHEPHEAA712 - 774184 - 246
24TRPTRPPHEPHEDC712 - 774184 - 246
15TRPTRPPHEPHEAA712 - 774184 - 246
25TRPTRPPHEPHEHE712 - 774184 - 246
16TRPTRPPHEPHEAA712 - 774184 - 246
26TRPTRPPHEPHELG712 - 774184 - 246
17ARGARGSERSERCB17 - 271 - 11
27ARGARGSERSERFD17 - 271 - 11
18ARGARGSERSERCB17 - 271 - 11
28ARGARGSERSERNH17 - 271 - 11
19PROPROLYSLYSDC530 - 7032 - 175
29PROPROLYSLYSHE530 - 7032 - 175
110PROPROLYSLYSDC530 - 7032 - 175
210PROPROLYSLYSLG530 - 7032 - 175
111ASNASNHISHISDC711 - 775183 - 247
211ASNASNHISHISHE711 - 775183 - 247
112ASNASNHISHISDC711 - 775183 - 247
212ASNASNHISHISLG711 - 775183 - 247
113ARGARGSERSERFD17 - 271 - 11
213ARGARGSERSERNH17 - 271 - 11
114PHEPHEARGARGHE529 - 7041 - 176
214PHEPHEARGARGLG529 - 7041 - 176
115ASNASNHISHISHE711 - 775183 - 247
215ASNASNHISHISLG711 - 775183 - 247

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Ancestral Glucocorticoid Receptor2


Mass: 28649.363 Da / Num. of mol.: 4
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: 1291.518 Da / Num. of mol.: 4
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
#3: Chemical
ChemComp-DEX / DEXAMETHASONE / 9A-FLUORO-16BETA-METHYLPREDNISOLONE


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
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: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.265
11K, H, -L20.24
11-K, -H, -L30.237
11-h,-k,l40.259
ReflectionResolution: 2.3→76.81 Å / Num. obs: 73686 / % possible obs: 94.4 % / Redundancy: 2.1 % / Biso Wilson estimate: 45 Å2 / CC1/2: 0.986 / Rpim(I) all: 0.079 / Rrim(I) all: 0.125 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.1 % / Num. unique obs: 10882 / CC1/2: 0.314 / Rpim(I) all: 0.641 / Rrim(I) all: 0.987 / % possible all: 95.6

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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: 2.3→76.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.003 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3765 5.1 %RANDOM
Rwork0.1773 ---
obs0.1795 69901 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 219.77 Å2 / Biso mean: 49.93 Å2 / Biso min: 11.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å2-0 Å2-0 Å2
2---1.77 Å2-0 Å2
3---3.55 Å2
Refinement stepCycle: final / Resolution: 2.3→76.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8156 0 113 8 8277
Biso mean--27.99 36.46 -
Num. residues----1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128458
X-RAY DIFFRACTIONr_angle_refined_deg2.0161.62511459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0425996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79322.329395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.874151560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.681544
X-RAY DIFFRACTIONr_chiral_restr0.1280.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026117
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A57530.08
12D57530.08
21A58140.08
22H58140.08
31A57530.08
32L57530.08
41A19400.08
42D19400.08
51A19440.08
52H19440.08
61A19160.09
62L19160.09
71C2630.12
72F2630.12
81C2660.11
82N2660.11
91D57510.08
92H57510.08
101D56950.08
102L56950.08
111D20120.09
112H20120.09
121D19940.09
122L19940.09
131F2660.16
132N2660.16
141H58040.08
142L58040.08
151H19960.09
152L19960.09
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.581 283 -
Rwork0.538 5195 -
all-5478 -
obs--95.67 %

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