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- PDB-5ufs: X-Ray Crystal Structure of the Ancestral Glucocorticoid Receptor ... -

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Basic information

Entry
Database: PDB / ID: 5ufs
TitleX-Ray Crystal Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with triamcinolone acetonide and SHP coregulator fragment
Components
  • Ancestral Glucocorticoid Receptor2
  • SHP NR Box 1 Peptide
KeywordsHORMONE RECEPTOR / Nuclear receptors / glucocorticoid receptor / ligand binding domain
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 / 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
Triamcinolone acetonide / 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: 2.118 Å
AuthorsWeikum, E.R. / Ortlund, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F31GM113397-01A1 United States
CitationJournal: Mol. Pharmacol. / Year: 2017
Title: Structural Analysis of the Glucocorticoid Receptor Ligand-Binding Domain in Complex with Triamcinolone Acetonide and a Fragment of the Atypical Coregulator, Small Heterodimer Partner.
Authors: Weikum, E.R. / Okafor, C.D. / D'Agostino, E.H. / Colucci, J.K. / Ortlund, E.A.
History
DepositionJan 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ancestral Glucocorticoid Receptor2
B: Ancestral Glucocorticoid Receptor2
C: SHP NR Box 1 Peptide
D: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2526
Polymers59,3834
Non-polymers8692
Water2,144119
1
A: Ancestral Glucocorticoid Receptor2
D: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1263
Polymers29,6922
Non-polymers4341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-13 kcal/mol
Surface area12350 Å2
MethodPISA
2
B: Ancestral Glucocorticoid Receptor2
C: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1263
Polymers29,6922
Non-polymers4341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-13 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.027, 52.829, 126.010
Angle α, β, γ (deg.)90.000, 101.780, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ancestral Glucocorticoid Receptor2


Mass: 28573.270 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X8XLE9*PLUS
#2: Protein/peptide SHP NR Box 1 Peptide


Mass: 1118.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15466*PLUS
#3: Chemical ChemComp-1TA / Triamcinolone acetonide / (4aS,4bR,5S,6aS,6bS,9aR,10aS,10bS)-4b-fluoro-5-hydroxy-6b-(hydroxyacetyl)-4a,6a,8,8-tetramethyl-4a,4b,5,6,6a,6b,9a,10,10a,10b,11,12-dodecahydro-2H,8H-naphtho[2',1':4,5]indeno[1,2-d][1,3]dioxol-2-one / Triamcinolone acetonide


Mass: 434.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H31FO6 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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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: 48.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES pH 7.5, 1.5 % glycerol, and 25 % PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 31952 / % possible obs: 98 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.04 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.11-2.1930.5580.865179.9
2.19-2.273.60.480.928199.9
2.27-2.383.60.3620.9451100
2.38-2.53.60.2790.963199.9
2.5-2.663.60.2150.978199.9
2.66-2.863.60.1510.9871100
2.86-3.153.70.120.991100
3.15-3.613.70.0840.9951100
3.61-4.543.70.0670.995199.9
4.54-503.50.0720.991199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXdev_2621refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GN8

3gn8


Resolution: 2.118→38.966 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 44.43
RfactorNum. reflection% reflection
Rfree0.2499 1590 5.01 %
Rwork0.2153 --
obs0.2172 31732 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.46 Å2 / Biso mean: 49.8495 Å2 / Biso min: 19.79 Å2
Refinement stepCycle: final / Resolution: 2.118→38.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4158 0 124 119 4401
Biso mean--34.73 41.01 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024316
X-RAY DIFFRACTIONf_angle_d0.5145858
X-RAY DIFFRACTIONf_chiral_restr0.034662
X-RAY DIFFRACTIONf_plane_restr0.002720
X-RAY DIFFRACTIONf_dihedral_angle_d8.3382598
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1176-2.18590.34391340.30212500263492
2.1859-2.26410.33941370.285327392876100
2.2641-2.35470.25511460.261927732919100
2.3547-2.46180.28181490.241627592908100
2.4618-2.59160.2781500.244327352885100
2.5916-2.75390.27371470.235527552902100
2.7539-2.96650.31251410.236827822923100
2.9665-3.26490.29251450.234327842929100
3.2649-3.7370.26691430.211827742917100
3.737-4.7070.20711490.161828012950100
4.707-38.97270.18141490.18382740288995
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6367-2.8935-1.1864.21472.94852.99820.32380.61470.187-0.5222-0.2369-0.5169-0.179-0.1207-0.03150.3277-0.01740.02550.42130.02590.330430.610533.38946.3322
28.2384-0.99861.65756.8645-0.7383.3356-0.16690.02340.5788-0.1481-0.1292-0.3193-0.66760.37570.28010.3558-0.0883-0.02760.4603-0.02660.3829.37450.605520.189
33.3218-1.586-0.65148.15453.40525.01870.08710.41590.2171-1.04980.0822-0.7869-0.53620.5963-0.14060.4127-0.05950.09080.61730.07620.50640.571637.82634.6409
44.90323.087-1.2571.7797-0.76870.58220.15960.7948-0.2995-0.0529-0.0025-0.16410.35620.18560.03070.194-0.07880.1860.26970.1460.28898.310229.502836.7012
53.96981.4089-0.4921.1321-1.12652.33710.12550.39430.0681-0.0257-0.0222-0.01440.2189-0.0427-0.19120.21040.023-0.01050.1786-0.11150.38210.784136.885637.071
64.27020.2857-0.77252.4892-0.19091.78540.0791-0.45750.14370.2296-0.011-0.07190.0125-0.0709-0.04190.23670.0128-0.00520.2734-0.05280.23918.475535.437745.2765
72.78662.6308-0.81752.8737-1.27841.48030.1281-0.59360.13960.2185-0.2987-0.0557-0.024-0.25950.10490.3875-0.0702-0.06040.43240.01650.283910.767933.19354.8926
84.9382-1.0812-0.02484.1941-0.99673.39330.214-0.0081-0.07030.0043-0.20650.4058-0.1658-0.3718-0.09260.305-0.0272-0.0150.2921-0.02660.326-5.976229.893948.023
96.5083-4.5194.39943.5589-2.45664.32680.20850.0931-0.17240.172-0.14170.19990.2873-0.2184-0.05990.422-0.13970.01250.29760.05190.3926-10.259720.951150.0279
101.83821.6332-0.9193.694-2.95072.98620.2414-0.37420.22211.15450.02480.232-0.43190.0303-0.25430.4314-0.00760.00890.3684-0.03270.3060.053333.38555.3412
114.4365-0.83810.61024.31881.12323.6132-0.08460.03620.03240.0883-0.0795-0.0954-0.3228-0.01850.14180.3683-0.0282-0.00880.13860.02220.41261.281950.613341.4814
126.02190.75770.06995.4163-4.23313.4843-0.0658-0.82360.78511.45810.27320.6628-1.0937-0.0866-0.04270.5554-0.04240.05740.558-0.06550.3034-9.91937.828357.0389
138.0747-1.97650.23291.7962-3.33318.19920.53360.9012-0.1979-0.09910.16640.15490.6035-0.18060.73930.15680.02990.03310.5179-0.03840.2501-8.791141.8531.4751
145.6119-0.0674-1.71164.54442.77184.68940.59330.0896-0.3260.0054-0.2359-0.0609-0.0797-0.11530.5740.3889-0.0851-0.07390.1579-0.09560.400739.474141.856830.1976
158.3948-6.3437-0.77884.68720.76650.7885-0.36880.0954-0.67290.09090.42790.38730.1020.01130.00790.29380.0188-0.12990.36140.1670.288422.347629.505524.9803
162.8129-0.94790.32992.6912-0.70192.0094-0.2499-0.12870.47120.39120.1807-0.2005-0.48550.07630.10170.30130.034-0.01130.3407-0.09940.194429.877136.891724.615
174.1895-1.5313-0.2280.9362-0.10592.1254-0.03-0.0835-0.0201-0.0814-0.03460.0525-0.0795-0.31860.01390.30850.06860.00240.2603-0.03310.253325.511833.58517.5676
183.72473.3708-3.1113.7103-4.70118.003-0.17351.37280.7482-0.07480.82990.30820.2783-0.0083-0.40420.40620.1522-0.03930.57860.09250.5379.95542.230112.2012
194.0717-2.5684-0.77792.7412.00092.580.38710.64650.0894-0.3715-0.2016-0.0123-0.17740.2032-0.06010.32810.0287-0.05090.45620.03610.29119.887133.18996.7839
205.28683.40360.98217.70490.01383.187-0.40190.74250.1357-0.38720.6116-0.1584-0.20730.1044-0.07490.2670.05520.03980.397-0.01810.283136.635929.887813.6583
217.93674.64415.15753.41493.9556.65560.26060.34880.12220.40740.16980.27080.60880.0314-0.46230.28840.0480.02540.4383-0.03910.390340.92520.966511.6573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 177 through 210 )A177 - 210
2X-RAY DIFFRACTION2chain 'A' and (resid 211 through 234 )A211 - 234
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 245 )A235 - 245
4X-RAY DIFFRACTION4chain 'B' and (resid -2 through 24 )B-2 - 24
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 57 )B25 - 57
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 108 )B58 - 108
7X-RAY DIFFRACTION7chain 'B' and (resid 109 through 125 )B109 - 125
8X-RAY DIFFRACTION8chain 'B' and (resid 126 through 151 )B126 - 151
9X-RAY DIFFRACTION9chain 'B' and (resid 152 through 176 )B152 - 176
10X-RAY DIFFRACTION10chain 'B' and (resid 177 through 210 )B177 - 210
11X-RAY DIFFRACTION11chain 'B' and (resid 211 through 234 )B211 - 234
12X-RAY DIFFRACTION12chain 'B' and (resid 235 through 245 )B235 - 245
13X-RAY DIFFRACTION13chain 'C' and (resid 17 through 27 )C17 - 27
14X-RAY DIFFRACTION14chain 'D' and (resid 17 through 27 )D17 - 27
15X-RAY DIFFRACTION15chain 'A' and (resid -2 through 24 )A-2 - 24
16X-RAY DIFFRACTION16chain 'A' and (resid 25 through 57 )A25 - 57
17X-RAY DIFFRACTION17chain 'A' and (resid 58 through 98 )A58 - 98
18X-RAY DIFFRACTION18chain 'A' and (resid 99 through 108 )A99 - 108
19X-RAY DIFFRACTION19chain 'A' and (resid 109 through 125 )A109 - 125
20X-RAY DIFFRACTION20chain 'A' and (resid 126 through 151 )A126 - 151
21X-RAY DIFFRACTION21chain 'A' and (resid 152 through 176 )A152 - 176

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