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- EMDB-23004: The GR-Maturation Complex: Glucocorticoid Receptor in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-23004
TitleThe GR-Maturation Complex: Glucocorticoid Receptor in complex with Hsp90 and co-chaperone p23
Map dataPrimary map ; GR:Hsp90:p23 ; sharpened, filtered, masked
Sample
  • Complex: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone p23
    • Protein or peptide: Heat shock protein HSP 90-alphaHeat shock response
    • Protein or peptide: Prostaglandin E synthase 3
    • Protein or peptide: Glucocorticoid receptor
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: DEXAMETHASONE
Function / homology
Function and homology information


lung saccule development / prostaglandin-E synthase / prostaglandin-E synthase activity / telomerase activity / Regulation of NPAS4 gene transcription / intracellular glucocorticoid receptor signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / Aryl hydrocarbon receptor signalling / steroid hormone binding ...lung saccule development / prostaglandin-E synthase / prostaglandin-E synthase activity / telomerase activity / Regulation of NPAS4 gene transcription / intracellular glucocorticoid receptor signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / Aryl hydrocarbon receptor signalling / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / microglia differentiation / cyclooxygenase pathway / maternal behavior / mammary gland duct morphogenesis / nucleus localization / telomerase holoenzyme complex / astrocyte differentiation / protein folding chaperone complex / glycogen biosynthetic process / cellular response to glucocorticoid stimulus / prostaglandin biosynthetic process / motor behavior / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / skin development / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / protein insertion into mitochondrial outer membrane / regulation of gluconeogenesis / adrenal gland development / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / cellular response to steroid hormone stimulus / Uptake and function of diphtheria toxin / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / chaperone cofactor-dependent protein refolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / skeletal muscle contraction / protein unfolding / regulation of protein-containing complex assembly / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / RHOBTB2 GTPase cycle / DNA polymerase binding / positive regulation of lamellipodium assembly / axonal growth cone / eNOS activation / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / positive regulation of phosphorylation / endocytic vesicle lumen / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle contraction / positive regulation of defense response to virus by host / Signaling by ERBB2 / Recruitment of mitotic centrosome proteins and complexes / cardiac muscle cell apoptotic process / response to salt stress / positive regulation of telomerase activity / cellular response to transforming growth factor beta stimulus / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane
Similarity search - Function
Co-chaperone protein p23-like / CS domain / CS domain / CS domain profile. / Glucocorticoid receptor / Glucocorticoid receptor / HSP20-like chaperone / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain ...Co-chaperone protein p23-like / CS domain / CS domain / CS domain profile. / Glucocorticoid receptor / Glucocorticoid receptor / HSP20-like chaperone / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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 / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Glucocorticoid receptor / Heat shock protein HSP 90-alpha / Prostaglandin E synthase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsNoddings CM / Wang Y-R / Agard DA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118099 United States
CitationJournal: Nature / Year: 2022
Title: Structure of Hsp90-p23-GR reveals the Hsp90 client-remodelling mechanism.
Authors: Chari M Noddings / Ray Yu-Ruei Wang / Jill L Johnson / David A Agard /
Abstract: Hsp90 is a conserved and essential molecular chaperone responsible for the folding and activation of hundreds of 'client' proteins. The glucocorticoid receptor (GR) is a model client that constantly ...Hsp90 is a conserved and essential molecular chaperone responsible for the folding and activation of hundreds of 'client' proteins. The glucocorticoid receptor (GR) is a model client that constantly depends on Hsp90 for activity. GR ligand binding was previously shown to nr inhibited by Hsp70 and restored by Hsp90, aided by the co-chaperone p23. However, a molecular understanding of the chaperone-mediated remodelling that occurs between the inactive Hsp70-Hsp90 'client-loading complex' and an activated Hsp90-p23 'client-maturation complex' is lacking for any client, including GR. Here we present a cryo-electron microscopy (cryo-EM) structure of the human GR-maturation complex (GR-Hsp90-p23), revealing that the GR ligand-binding domain is restored to a folded, ligand-bound conformation, while being simultaneously threaded through the Hsp90 lumen. In addition, p23 directly stabilizes native GR using a C-terminal helix, resulting in enhanced ligand binding. This structure of a client bound to Hsp90 in a native conformation contrasts sharply with the unfolded kinase-Hsp90 structure. Thus, aided by direct co-chaperone-client interactions, Hsp90 can directly dictate client-specific folding outcomes. Together with the GR-loading complex structure, we present the molecular mechanism of chaperone-mediated GR remodelling, establishing the first, to our knowledge, complete chaperone cycle for any Hsp90 client.
History
DepositionNov 20, 2020-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateJan 26, 2022-
Current statusJan 26, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
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  • Surface view with fitted model
  • Atomic models: PDB-7krj
  • Surface level: 0.015
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23004.png

Downloads & links

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Map

FileDownload / File: emd_23004.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map ; GR:Hsp90:p23 ; sharpened, filtered, masked
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.025896722 - 0.12167934
Average (Standard dev.)0.00020637564 (±0.0020969005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 250.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8350.8350.835
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z250.500250.500250.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0260.1220.000

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Supplemental data

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Mask #1

Fileemd_23004_msk_1.map
Projections & Slices
AxesZYX

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Mask #2

Fileemd_23004_msk_2.map
Projections & Slices
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Additional map: Raw GR:Hsp90:p23 map

Fileemd_23004_additional_1.map
AnnotationRaw GR:Hsp90:p23 map
Projections & Slices
AxesZYX

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Additional map: Composite map of GR:Hsp90:p23

Fileemd_23004_additional_2.map
AnnotationComposite map of GR:Hsp90:p23
Projections & Slices
AxesZYX

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Additional map: Focused map for GR:Hsp90:p23 ; focused on GR:p23 tail

Fileemd_23004_additional_3.map
AnnotationFocused map for GR:Hsp90:p23 ; focused on GR:p23 tail
Projections & Slices
AxesZYX

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Half map: GR:Hsp90:p23 Half Map 1

Fileemd_23004_half_map_1.map
AnnotationGR:Hsp90:p23 Half Map 1
Projections & Slices
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Half map: GR:Hsp90:p23 Half Map 2

Fileemd_23004_half_map_2.map
AnnotationGR:Hsp90:p23 Half Map 2
Projections & Slices
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Sample components

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Entire : Complex of the Glucocorticoid Receptor ligand binding domain, Hsp...

EntireName: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone p23
Components
  • Complex: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone p23
    • Protein or peptide: Heat shock protein HSP 90-alphaHeat shock response
    • Protein or peptide: Prostaglandin E synthase 3
    • Protein or peptide: Glucocorticoid receptor
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: DEXAMETHASONE

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Supramolecule #1: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp...

SupramoleculeName: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone p23
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
Molecular weightTheoretical: 263 KDa

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Macromolecule #1: Heat shock protein HSP 90-alpha

MacromoleculeName: Heat shock protein HSP 90-alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.781727 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MPEETQTQDQ PMEEEEVETF AFQAEIAQLM SLIINTFYSN KEIFLRELIS NSSDALDKIR YESLTDPSKL DSGKELHINL IPNKQDRTL TIVDTGIGMT KADLINNLGT IAKSGTKAFM EALQAGADIS MIGQFGVGFY SAYLVAEKVT VITKHNDDEQ Y AWESSAGG ...String:
MPEETQTQDQ PMEEEEVETF AFQAEIAQLM SLIINTFYSN KEIFLRELIS NSSDALDKIR YESLTDPSKL DSGKELHINL IPNKQDRTL TIVDTGIGMT KADLINNLGT IAKSGTKAFM EALQAGADIS MIGQFGVGFY SAYLVAEKVT VITKHNDDEQ Y AWESSAGG SFTVRTDTGE PMGRGTKVIL HLKEDQTEYL EERRIKEIVK KHSQFIGYPI TLFVEKERDK EVSDDEAEEK ED KEEEKEK EEKESEDKPE IEDVGSDEEE EKKDGDKKKK KKIKEKYIDQ EELNKTKPIW TRNPDDITNE EYGEFYKSLT NDW EDHLAV KHFSVEGQLE FRALLFVPRR APFDLFENRK KKNNIKLYVR RVFIMDNCEE LIPEYLNFIR GVVDSEDLPL NISR EMLQQ SKILKVIRKN LVKKCLELFT ELAEDKENYK KFYEQFSKNI KLGIHEDSQN RKKLSELLRY YTSASGDEMV SLKDY CTRM KENQKHIYYI TGETKDQVAN SAFVERLRKH GLEVIYMIEP IDEYCVQQLK EFEGKTLVSV TKEGLELPED EEEKKK QEE KKTKFENLCK IMKDILEKKV EKVVVSNRLV TSPCCIVTST YGWTANMERI MKAQALRDNS TMGYMAAKKH LEINPDH SI IETLRQKAEA DKNDKSVKDL VILLYETALL SSGFSLEDPQ THANRIYRMI KLGLGIDEDD PTADDTSAAV TEEMPPLE G DDDTSRMEEV D

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Macromolecule #2: Prostaglandin E synthase 3

MacromoleculeName: Prostaglandin E synthase 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: prostaglandin-E synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.720395 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MQPASAKWYD RRDYVFIEFC VEDSKDVNVN FEKSKLTFSC LGGSDNFKHL NEIDLFHCID PNDSKHKRTD RSILCCLRKG ESGQSWPRL TKERAKLNWL SVDFNNWKDW EDDSDEDMSN FDRFSEMMNN MGGDEDVDLP EVDGADDDSQ DSDDEKMPDL E

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Macromolecule #3: Glucocorticoid receptor

MacromoleculeName: Glucocorticoid receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.924867 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: IVPATLPQLT PTLVSLLEVI EPEVLYAGYD SSVPDSTWRI MTTLNMLGGR QVIAAVKWAK AIPGFRNLHL DDQMTLLQYS WMSLMAFAL GWRSYRQSSA NLLCFAPDLI INEQRMTLPC MYDQCKHMLY VSSELHRLQV SYEEYLCMKT LLLLSSVPKD G LKSQELFD ...String:
IVPATLPQLT PTLVSLLEVI EPEVLYAGYD SSVPDSTWRI MTTLNMLGGR QVIAAVKWAK AIPGFRNLHL DDQMTLLQYS WMSLMAFAL GWRSYRQSSA NLLCFAPDLI INEQRMTLPC MYDQCKHMLY VSSELHRLQV SYEEYLCMKT LLLLSSVPKD G LKSQELFD EIRMTYIKEL GKAIVKREGN SSQNWQRFYQ LTKLLDSMHE VVENLLNYCF QTFLDKTMSI EFPEMLAEII TN QIPKYSN GNIKKLLFHQ K

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: DEXAMETHASONE

MacromoleculeName: DEXAMETHASONE / type: ligand / ID: 6 / Number of copies: 1 / Formula: DEX
Molecular weightTheoretical: 392.461 Da
Chemical component information

ChemComp-DEX:
DEXAMETHASONE / medication, antibiotic*YM / Dexamethasone

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 5608 / Average exposure time: 5.9 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6062152
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2cg9

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 140217
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5fwk

chain_id: A

5fwk

chain_id: B

1m2z

chain_id: A

1ejf

chain_id: A
Output model

PDB-7krj:
The GR-Maturation Complex: Glucocorticoid Receptor in complex with Hsp90 and co-chaperone p23

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