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- PDB-6nwl: Structure of the Ancestral Glucocorticoid Receptor 2 ligand bindi... -

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Basic information

Entry
Database: PDB / ID: 6nwl
TitleStructure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with hydrocortisone and PGC1a coregulator fragment
Components
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
  • glucocorticoid receptor
KeywordsHORMONE / glucocorticoid receptor / agonist / coactivator
Function / homology
Function and homology information


positive regulation of fatty acid oxidation / : / lncRNA binding / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / temperature homeostasis / intracellular glucose homeostasis / response to starvation / fatty acid oxidation ...positive regulation of fatty acid oxidation / : / lncRNA binding / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / temperature homeostasis / intracellular glucose homeostasis / response to starvation / fatty acid oxidation / response to dietary excess / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / energy homeostasis / brown fat cell differentiation / positive regulation of gluconeogenesis / digestion / respiratory electron transport chain / mitochondrion organization / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / gluconeogenesis / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / negative regulation of smooth muscle cell proliferation / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / chromatin DNA binding / mRNA processing / PML body / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Regulation of RUNX2 expression and activity / Circadian Clock / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / protein-containing complex assembly / DNA-binding transcription factor binding / neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / sequence-specific DNA binding / transcription coactivator activity / protein stabilization / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily ...PGC-1alpha, RNA recognition motif / PGC-1 / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-HCY / THIOCYANATE ION / L(+)-TARTARIC ACID / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.595 Å
AuthorsLiu, X. / Ortlund, E.A.
Funding support United States, 2items
OrganizationGrant numberCountry
American Heart Association17POST33660110 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)5R01DK115213 United States
CitationJournal: Mol.Pharmacol. / Year: 2019
Title: First High-Resolution Crystal Structures of the Glucocorticoid Receptor Ligand-Binding Domain-Peroxisome Proliferator-ActivatedgammaCoactivator 1-alphaComplex with Endogenous and Synthetic Glucocorticoids.
Authors: Liu, X. / Wang, Y. / Ortlund, E.A.
History
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: glucocorticoid receptor
B: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,18710
Polymers30,0442
Non-polymers1,1438
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-10 kcal/mol
Surface area12420 Å2
Unit cell
Length a, b, c (Å)71.756, 96.435, 108.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein glucocorticoid receptor


Mass: 28778.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1265.627 Da / Num. of mol.: 1 / Fragment: UNP Residues 141-152 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2

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Non-polymers , 6 types, 98 molecules

#3: Chemical ChemComp-HCY / (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione / CORTISOL


Mass: 362.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, hormone*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.05 M sodium thiocyanate, 0.95 M sodium tartrate dibasic dehydrate and 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.595→50 Å / Num. obs: 50002 / % possible obs: 99.6 % / Redundancy: 11.7 % / Biso Wilson estimate: 28.53 Å2 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.209 / Χ2: 0.969 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6611.21.87549230.7010.5721.9620.79999.5
1.66-1.7211.81.46850050.8120.4371.5330.82599.8
1.72-1.811.71.07649370.8840.3221.1240.86799.9
1.8-1.911.20.71749450.9420.2210.7510.99599.5
1.9-2.0210.60.43849510.9670.1390.461.0299.5
2.02-2.1712.70.27749900.9840.080.2891.054100
2.17-2.3912.20.17849980.990.0520.1851.0899.9
2.39-2.7411.10.11949940.9940.0370.1250.99299.3
2.74-3.4512.60.10450550.9950.030.1080.99499.8
3.45-50120.21752040.9550.0650.2271.03899.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 1.595→39.422 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.7
RfactorNum. reflection% reflection
Rfree0.193 2000 4 %
Rwork0.1787 --
obs0.1793 49964 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.05 Å2 / Biso mean: 37.2977 Å2 / Biso min: 17.73 Å2
Refinement stepCycle: final / Resolution: 1.595→39.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 150 90 2337
Biso mean--52.59 40.04 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062366
X-RAY DIFFRACTIONf_angle_d0.8063220
X-RAY DIFFRACTIONf_chiral_restr0.047361
X-RAY DIFFRACTIONf_plane_restr0.004400
X-RAY DIFFRACTIONf_dihedral_angle_d16.7741438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5946-1.63440.29551360.2873262339896
1.6344-1.67860.25691420.247233963538100
1.6786-1.7280.2281420.214434153557100
1.728-1.78380.24021420.194933983540100
1.7838-1.84760.22461420.187134013543100
1.8476-1.92150.191410.18433395353699
1.9215-2.0090.22121430.187434263569100
2.009-2.11490.22191430.180134193562100
2.1149-2.24740.22851430.177934413584100
2.2474-2.42090.19891440.178434393583100
2.4209-2.66450.17561430.183834403583100
2.6645-3.04990.22051440.18413441358599
3.0499-3.8420.17351450.174334983643100
3.842-39.43450.17251500.1663593374399
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)
11.50660.9305-0.53221.58390.94612.009-0.2977-0.7053-0.14380.52650.2777-0.07260.1621-0.2456-0.00080.3299-0.0638-00.37280.04770.3246-9.8309-26.355814.8432
21.3186-0.0850.06721.2811-0.13610.81640.0342-0.0062-0.16670.018-0.01590.07930.184-0.04070.00010.2146-0.0164-0.00180.21920.00770.2125-3.8496-26.40728.524
31.18090.4304-0.76571.34330.78591.4837-0.0582-0.2294-0.10030.28930.0871-0.29090.07050.3545-0.00040.277-0.0055-0.02860.30260.0210.2883.3469-18.357514.7789
41.6419-0.65810.14232.443-0.50921.11730.00990.12510.0346-0.00630.0081-0.05730.00010.0549-0.00010.2129-0.03050.02580.25690.02610.22560.3363-17.73910.5114
50.04450.03720.01770.1924-0.10340.0949-0.3740.5305-0.4050.05710.02950.54570.2288-0.36070.00220.4579-0.112-0.08380.347-0.06810.4831-12.3746-35.2732-3.5456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 24 )A-2 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 98 )A25 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 140 )A99 - 140
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 246 )A141 - 246
5X-RAY DIFFRACTION5chain 'B' and (resid 141 through 152 )B141 - 152

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