+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29069 | |||||||||
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Title | Cryo-EM structure of the GR-Hsp90-FKBP51 complex | |||||||||
Map data | Sharpened consensus map for the GR-Hsp90-FKBP51 complex | |||||||||
Sample |
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Keywords | chaperone / steroid hormone receptor / ligand binding / ATP binding / protein folding | |||||||||
Function / homology | Function and homology information Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / astrocyte differentiation / cellular response to glucocorticoid stimulus / motor behavior / positive regulation of tau-protein kinase activity / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / protein insertion into mitochondrial outer membrane / adrenal gland development / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / regulation of gluconeogenesis / cellular response to steroid hormone stimulus / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / FK506 binding / 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 / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / protein unfolding / telomere maintenance via telomerase / HSF1-dependent transactivation / response to unfolded protein / positive regulation of cell size / chaperone-mediated protein complex assembly / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / estrogen response element binding / RHOBTB2 GTPase cycle / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of defense response to virus by host / eNOS activation / axonal growth cone / positive regulation of lamellipodium assembly / nuclear receptor-mediated steroid hormone signaling pathway / DNA polymerase binding / core promoter sequence-specific DNA binding / MECP2 regulates neuronal receptors and channels / activation of innate immune response / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / cellular response to transforming growth factor beta stimulus / chaperone-mediated protein folding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Signaling by ERBB2 / heat shock protein binding / response to salt stress / cardiac muscle cell apoptotic process / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / positive regulation of cardiac muscle contraction / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / TBP-class protein binding / response to cold / protein tyrosine kinase binding / lysosomal lumen / AURKA Activation by TPX2 / Constitutive Signaling by Overexpressed ERBB2 / cellular response to dexamethasone stimulus / ESR-mediated signaling Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Noddings CM / Agard DA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Cryo-EM reveals how Hsp90 and FKBP immunophilins co-regulate the glucocorticoid receptor. Authors: Chari M Noddings / Jill L Johnson / David A Agard / Abstract: Hsp90 is an essential molecular chaperone responsible for the folding and activation of hundreds of 'client' proteins, including the glucocorticoid receptor (GR). Previously, we revealed that Hsp70 ...Hsp90 is an essential molecular chaperone responsible for the folding and activation of hundreds of 'client' proteins, including the glucocorticoid receptor (GR). Previously, we revealed that Hsp70 and Hsp90 remodel the conformation of GR to regulate ligand binding, aided by co-chaperones. In vivo, the co-chaperones FKBP51 and FKBP52 antagonistically regulate GR activity, but a molecular understanding is lacking. Here we present a 3.01 Å cryogenic electron microscopy structure of the human GR:Hsp90:FKBP52 complex, revealing how FKBP52 integrates into the GR chaperone cycle and directly binds to the active client, potentiating GR activity in vitro and in vivo. We also present a 3.23 Å cryogenic electron microscopy structure of the human GR:Hsp90:FKBP51 complex, revealing how FKBP51 competes with FKBP52 for GR:Hsp90 binding and demonstrating how FKBP51 can act as a potent antagonist to FKBP52. Altogether, we demonstrate how FKBP51 and FKBP52 integrate into the GR chaperone cycle to advance GR to the next stage of maturation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29069.map.gz | 64 MB | EMDB map data format | |
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Header (meta data) | emd-29069-v30.xml emd-29069.xml | 31.9 KB 31.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29069_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_29069.png | 72 KB | ||
Masks | emd_29069_msk_1.map emd_29069_msk_2.map emd_29069_msk_3.map | 125 MB 125 MB 125 MB | Mask map | |
Filedesc metadata | emd-29069.cif.gz | 7.6 KB | ||
Others | emd_29069_additional_1.map.gz emd_29069_additional_2.map.gz emd_29069_additional_3.map.gz emd_29069_additional_4.map.gz emd_29069_half_map_1.map.gz emd_29069_half_map_2.map.gz | 117.8 MB 62.4 MB 117.9 MB 117.3 MB 116.2 MB 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29069 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29069 | HTTPS FTP |
-Validation report
Summary document | emd_29069_validation.pdf.gz | 918.4 KB | Display | EMDB validaton report |
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Full document | emd_29069_full_validation.pdf.gz | 918 KB | Display | |
Data in XML | emd_29069_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_29069_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29069 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29069 | HTTPS FTP |
-Related structure data
Related structure data | 8ffwMC 8ffvC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29069.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened consensus map for the GR-Hsp90-FKBP51 complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29069_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_29069_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #3
File | emd_29069_msk_3.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Focused map on GR-FKBP51 in the GR-Hsp90-FKBP51 complex
File | emd_29069_additional_1.map | ||||||||||||
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Annotation | Focused map on GR-FKBP51 in the GR-Hsp90-FKBP51 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened consensus map for GR-Hsp90-FKBP51
File | emd_29069_additional_2.map | ||||||||||||
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Annotation | Unsharpened consensus map for GR-Hsp90-FKBP51 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused map on Hsp90 in the GR-Hsp90-FKBP51 complex
File | emd_29069_additional_3.map | ||||||||||||
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Annotation | Focused map on Hsp90 in the GR-Hsp90-FKBP51 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Composite map for the GR-Hsp90-FKBP51 complex made from...
File | emd_29069_additional_4.map | ||||||||||||
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Annotation | Composite map for the GR-Hsp90-FKBP51 complex made from the Hsp90 focused map and GR-FKBP51 focused map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 for the GR-Hsp90-FKBP51 consensus map
File | emd_29069_half_map_1.map | ||||||||||||
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Annotation | Half map 1 for the GR-Hsp90-FKBP51 consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 for the GR-Hsp90-FKBP51 consensus map
File | emd_29069_half_map_2.map | ||||||||||||
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Annotation | Half map 2 for the GR-Hsp90-FKBP51 consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of the Glucocorticoid Receptor ligand binding domain, Hsp...
Entire | Name: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone FKBP51 |
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Components |
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-Supramolecule #1: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp...
Supramolecule | Name: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone FKBP51 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 306.5 KDa |
-Macromolecule #1: Heat shock protein HSP 90-alpha
Macromolecule | Name: Heat shock protein HSP 90-alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-chaperonin molecular chaperone ATPase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 84.650531 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: PEETQTQDQP MEEEEVETFA FQAEIAQLMS LIINTFYSNK EIFLRELISN SSDALDKIRY ESLTDPSKLD SGKELHINLI PNKQDRTLT IVDTGIGMTK ADLINNLGTI AKSGTKAFME ALQAGADISM IGQFGVGFYS AYLVAEKVTV ITKHNDDEQY A WESSAGGS ...String: PEETQTQDQP MEEEEVETFA FQAEIAQLMS LIINTFYSNK EIFLRELISN SSDALDKIRY ESLTDPSKLD SGKELHINLI PNKQDRTLT IVDTGIGMTK ADLINNLGTI AKSGTKAFME ALQAGADISM IGQFGVGFYS AYLVAEKVTV ITKHNDDEQY A WESSAGGS FTVRTDTGEP MGRGTKVILH LKEDQTEYLE ERRIKEIVKK HSQFIGYPIT LFVEKERDKE VSDDEAEEKE DK EEEKEKE EKESEDKPEI EDVGSDEEEE KKDGDKKKKK KIKEKYIDQE ELNKTKPIWT RNPDDITNEE YGEFYKSLTN DWE DHLAVK HFSVEGQLEF RALLFVPRRA PFDLFENRKK KNNIKLYVRR VFIMDNCEEL IPEYLNFIRG VVDSEDLPLN ISRE MLQQS KILKVIRKNL VKKCLELFTE LAEDKENYKK FYEQFSKNIK LGIHEDSQNR KKLSELLRYY TSASGDEMVS LKDYC TRMK ENQKHIYYIT GETKDQVANS AFVERLRKHG LEVIYMIEPI DEYCVQQLKE FEGKTLVSVT KEGLELPEDE EEKKKQ EEK KTKFENLCKI MKDILEKKVE KVVVSNRLVT SPCCIVTSTY GWTANMERIM KAQALRDNST MGYMAAKKHL EINPDHS II ETLRQKAEAD KNDKSVKDLV ILLYETALLS SGFSLEDPQT HANRIYRMIK LGLGIDEDDP TADDTSAAVT EEMPPLEG D DDTSRMEEVD UniProtKB: Heat shock protein HSP 90-alpha |
-Macromolecule #2: Glucocorticoid receptor
Macromolecule | Name: Glucocorticoid receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.198973 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: PKLCLVCSDE ASGCHYGVLT CGSCKVFFKR AVEGQHNYLC AGRNDCIIDK IRRKNCPACR YRKCLQAGMN LEARKTKKKI KGIQQATTG VSQETSENPG NKTIVPATLP QLTPTLVSLL EVIEPEVLYA GYDSSVPDST WRIMTTLNML GGRQVIAAVK W AKAIPGFR ...String: PKLCLVCSDE ASGCHYGVLT CGSCKVFFKR AVEGQHNYLC AGRNDCIIDK IRRKNCPACR YRKCLQAGMN LEARKTKKKI KGIQQATTG VSQETSENPG NKTIVPATLP QLTPTLVSLL EVIEPEVLYA GYDSSVPDST WRIMTTLNML GGRQVIAAVK W AKAIPGFR NLHLDDQMTL LQYSWMSLMA FALGWRSYRQ SSANLLCFAP DLIINEQRMT LPCMYDQCKH MLYVSSELHR LQ VSYEEYL CMKTLLLLSS VPKDGLKSQE LFDEIRMTYI KELGKAIVKR EGNSSQNWQR FYQLTKLLDS MHEVVENLLN YCF QTFLDK TMSIEFPEML AEIITNQIPK YSNGNIKKLL FHQK UniProtKB: Glucocorticoid receptor |
-Macromolecule #3: Peptidyl-prolyl cis-trans isomerase FKBP5
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase FKBP5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 51.158992 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: TTDEGAKNNE ESPTATVAEQ GEDITSKKDR GVLKIVKRVG NGEETPMIGD KVYVHYKGKL SNGKKFDSSH DRNEPFVFSL GKGQVIKAW DIGVATMKKG EICHLLCKPE YAYGSAGSLP KIPSNATLFF EIELLDFKGE DLFEDGGIIR RTKRKGEGYS N PNEGATVE ...String: TTDEGAKNNE ESPTATVAEQ GEDITSKKDR GVLKIVKRVG NGEETPMIGD KVYVHYKGKL SNGKKFDSSH DRNEPFVFSL GKGQVIKAW DIGVATMKKG EICHLLCKPE YAYGSAGSLP KIPSNATLFF EIELLDFKGE DLFEDGGIIR RTKRKGEGYS N PNEGATVE IHLEGRCGGR MFDCRDVAFT VGEGEDHDIP IGIDKALEKM QREEQCILYL GPRYGFGEAG KPKFGIEPNA EL IYEVTLK SFEKAKESWE MDTKEKLEQA AIVKEKGTVY FKGGKYMQAV IQYGKIVSWL EMEYGLSEKE SKASESFLLA AFL NLAMCY LKLREYTKAV ECCDKALGLD SANEKGLYRR GEAQLLMNEF ESAKGDFEKV LEVNPQNKAA RLQISMCQKK AKEH NERDR RIYANMFKKF AEQDAKEEAN KAMGKKTSEG VTNEKGTDSQ AMEEEKPEGH V UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP5 |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: DEXAMETHASONE
Macromolecule | Name: DEXAMETHASONE / type: ligand / ID: 6 / Number of copies: 1 / Formula: DEX |
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Molecular weight | Theoretical: 392.461 Da |
Chemical component information | ChemComp-DEX: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 5489 / #0 - Average exposure time: 3.0 sec. / #0 - Average electron dose: 69.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Number grids imaged: 1 / #1 - Number real images: 20924 / #1 - Average exposure time: 2.0 sec. / #1 - Average electron dose: 45.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Output model | PDB-8ffw: |