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- PDB-7prv: The glucocorticoid receptor in complex with fluticasone furoate, ... -

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Basic information

Entry
Database: PDB / ID: 7prv
TitleThe glucocorticoid receptor in complex with fluticasone furoate, a PGC1a coactivator fragment and sgk 23bp
Components
  • DNA (5'-D(*TP*AP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*GP*TP*CP*GP*A)-3')
  • DNA (5'-D(*TP*CP*GP*AP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*TP*GP*TP*A)-3')
  • Glucocorticoid receptor
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsSIGNALING PROTEIN / nuclear receptor / ligand-activated transcription factor / multi-domain / complex / agonist
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / glucocorticoid metabolic process / response to cortisol / PTK6 Expression / neuroinflammatory response / positive regulation of fatty acid oxidation ...Regulation of MITF-M dependent genes involved in metabolism / Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / glucocorticoid metabolic process / response to cortisol / PTK6 Expression / neuroinflammatory response / positive regulation of fatty acid oxidation / mammary gland duct morphogenesis / microglia differentiation / cellular respiration / maternal behavior / astrocyte differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / adrenal gland development / cellular response to glucocorticoid stimulus / regulation of gluconeogenesis / cellular response to steroid hormone stimulus / temperature homeostasis / response to starvation / lncRNA binding / response to muscle activity / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / motor behavior / estrogen response element binding / cellular response to dexamethasone stimulus / adipose tissue development / nuclear receptor-mediated steroid hormone signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to transforming growth factor beta stimulus / brown fat cell differentiation / core promoter sequence-specific DNA binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / energy homeostasis / digestion / steroid binding / positive regulation of gluconeogenesis / RNA splicing / SUMOylation of transcription cofactors / TBP-class protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nuclear receptor binding / gluconeogenesis / respiratory electron transport chain / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mitochondrion organization / chromosome segregation / synaptic transmission, glutamatergic / transcription initiation at RNA polymerase II promoter / SUMOylation of intracellular receptors / promoter-specific chromatin binding / negative regulation of smooth muscle cell proliferation / Hsp90 protein binding / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / PML body / chromatin DNA binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / response to wounding / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / mRNA processing / nuclear receptor activity / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / : / positive regulation of neuron apoptotic process / positive regulation of cold-induced thermogenesis / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / cellular response to oxidative stress / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / DNA-binding transcription factor binding / sequence-specific DNA binding / Potential therapeutics for SARS / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / protein stabilization / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mitochondrial matrix / DNA-binding transcription factor activity / cell division / negative regulation of DNA-templated transcription / apoptotic process
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Glucocorticoid receptor / Glucocorticoid receptor / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...PGC-1alpha, RNA recognition motif / PGC-1 / Glucocorticoid receptor / Glucocorticoid receptor / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / 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 / Zinc finger, NHR/GATA-type / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Chem-GW6 / DNA / DNA (> 10) / Glucocorticoid receptor / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPostel, S. / Edman, K. / Wissler, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Quaternary glucocorticoid receptor structure highlights allosteric interdomain communication.
Authors: Postel, S. / Wissler, L. / Johansson, C.A. / Gunnarsson, A. / Gordon, E. / Collins, B. / Castaldo, M. / Kohler, C. / Oling, D. / Johansson, P. / Froderberg Roth, L. / Beinsteiner, B. / ...Authors: Postel, S. / Wissler, L. / Johansson, C.A. / Gunnarsson, A. / Gordon, E. / Collins, B. / Castaldo, M. / Kohler, C. / Oling, D. / Johansson, P. / Froderberg Roth, L. / Beinsteiner, B. / Dainty, I. / Delaney, S. / Klaholz, B.P. / Billas, I.M.L. / Edman, K.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucocorticoid receptor
B: Glucocorticoid receptor
C: DNA (5'-D(*TP*CP*GP*AP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*TP*GP*TP*A)-3')
D: DNA (5'-D(*TP*AP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*GP*TP*CP*GP*A)-3')
F: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,89014
Polymers105,3655
Non-polymers1,5259
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-29 kcal/mol
Surface area36210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.674, 119.725, 135.527
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*TP*CP*GP*AP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*TP*GP*TP*A)-3')


Mass: 7064.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*AP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*GP*TP*CP*GP*A)-3')


Mass: 7015.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein / Protein/peptide , 2 types, 3 molecules ABF

#1: Protein Glucocorticoid receptor / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 44511.457 Da / Num. of mol.: 2 / Mutation: S404A, N517D, V571M, F602S, C638D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04150
#4: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PGC-1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6 / PGC1a ...PGC-1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6 / PGC1a coactivator fragment


Mass: 2261.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2

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Non-polymers , 4 types, 39 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GW6 / (6alpha,11alpha,14beta,16alpha,17alpha)-6,9-difluoro-17-{[(fluoromethyl)sulfanyl]carbonyl}-11-hydroxy-16-methyl-3-oxoan drosta-1,4-dien-17-yl furan-2-carboxylate / Fluticasone furoate


Mass: 538.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H29F3O6S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.02 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8 % PEG3350, 0.3 M 1,6-hexanediol, 0.1 M guanidine hydrochloride, 8 % 2,2,2-trifluoroethanol, 0.1 M Bis Tris Propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96545 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96545 Å / Relative weight: 1
ReflectionResolution: 2.7→68.684 Å / Num. obs: 24963 / % possible obs: 93.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Net I/σ(I): 16.3
Reflection shellResolution: 2.7→3.005 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1248 / Rpim(I) all: 0.425 / % possible all: 63.5

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROC1.1.7data processing
autoPROC1.1.7data scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3g9O, 4P6W

3g9o

4p6w


Resolution: 2.7→68.68 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.382
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 1240 -RANDOM
Rwork0.2141 ---
obs0.2161 24963 68.7 %-
Displacement parametersBiso mean: 103.55 Å2
Baniso -1Baniso -2Baniso -3
1-5.1407 Å20 Å20 Å2
2---6.6956 Å20 Å2
3---1.5548 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→68.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5262 896 90 30 6278
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086463HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.928925HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2157SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes945HARMONIC5
X-RAY DIFFRACTIONt_it6463HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion836SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4911SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion20.33
LS refinement shellResolution: 2.7→2.88 Å
RfactorNum. reflection% reflection
Rfree0.3673 29 -
Rwork0.3125 --
obs0.3161 500 8 %
Refinement TLS params.

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)
16.52086.2242-0.767611.57060.04854.1108-0.2804-0.11240.1148-0.11240.3657-1.04780.1148-1.0478-0.0853-0.2587-0.1443-0.25650.0655-0.08070.0643-1.687-9.1424-14.3638
28.4483-4.9915-1.603710.45581.23184.37760.46940.3721-0.50540.37210.2573-0.6031-0.5054-0.6031-0.72680.27660.19160.25860.2373-0.04890.46390.797214.5871-7.1795
31.43621.2189-0.013410.09481.57763.60070.24371.31270.02751.3127-0.6127-1.26640.0275-1.26640.369-0.3373-0.00540.1214-0.5503-0.10170.499-14.0308-0.1222-2.5777
41.34161.5183-0.172817.3250.81753.63340.43681.52360.181.5236-0.6023-1.3470.18-1.3470.1655-0.3940.02180.1622-0.562-0.09970.4556-14.15940.3564-3.1937
54.39330.295-0.47857.0182-2.26.9393-0.1545-0.45540.276-0.4554-0.22671.42380.2761.42380.3812-0.5385-0.01730.0526-0.2127-0.0614-0.57629.7537-0.5078-11.7711
62.8140.5063-0.35416.3053-2.423911.52380.31960.6531-1.7790.6531-0.86322.4612-1.7792.46120.5436-0.4649-0.4045-0.1714-0.1146-0.0174-0.919827.24850.645521.9575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|417-488 }A417 - 488
2X-RAY DIFFRACTION2{ B|418-488 }B418 - 488
3X-RAY DIFFRACTION3{ C|* }C1 - 22
4X-RAY DIFFRACTION4{ D|* }D1 - 22
5X-RAY DIFFRACTION5{ A|528-776 }A528 - 776
6X-RAY DIFFRACTION6{ B|527-776 }B527 - 776

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