+Open data
-Basic information
Entry | Database: PDB / ID: 8gae | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Hsp90 provides platform for CRaf dephosphorylation by PP5 | |||||||||||||||
Components |
| |||||||||||||||
Keywords | CHAPERONE / kinase / phosphatase / complex | |||||||||||||||
Function / homology | Function and homology information regulation of type II interferon-mediated signaling pathway / response to arachidonate / receptor ligand inhibitor activity / HSP90-CDC37 chaperone complex / death-inducing signaling complex assembly / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / peptidyl-serine dephosphorylation / : / peptidyl-threonine dephosphorylation ...regulation of type II interferon-mediated signaling pathway / response to arachidonate / receptor ligand inhibitor activity / HSP90-CDC37 chaperone complex / death-inducing signaling complex assembly / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / peptidyl-serine dephosphorylation / : / peptidyl-threonine dephosphorylation / aryl hydrocarbon receptor complex / intermediate filament cytoskeleton organization / dynein axonemal particle / regulation of Rho protein signal transduction / histone methyltransferase binding / type B pancreatic cell proliferation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of protein localization to cell surface / ATP-dependent protein binding / Rap1 signalling / regulation of cell motility / protein kinase regulator activity / insulin secretion involved in cellular response to glucose stimulus / protein folding chaperone complex / response to morphine / Negative feedback regulation of MAPK pathway / post-transcriptional regulation of gene expression / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / GP1b-IX-V activation signalling / protein serine/threonine phosphatase activity / activation of adenylate cyclase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / IFNG signaling activates MAPKs / 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 / myosin phosphatase activity / TPR domain binding / protein-serine/threonine phosphatase / regulation of cell differentiation / ERBB2-ERBB3 signaling pathway / Assembly and release of respiratory syncytial virus (RSV) virions / positive regulation of transforming growth factor beta receptor signaling pathway / pseudopodium / face development / dendritic growth cone / somatic stem cell population maintenance / phosphatase activity / regulation of type I interferon-mediated signaling pathway / : / The NLRP3 inflammasome / neurotrophin TRK receptor signaling pathway / phosphoprotein phosphatase activity / thyroid gland development / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / telomere maintenance via telomerase / HSF1-dependent transactivation / response to unfolded protein / extrinsic apoptotic signaling pathway via death domain receptors / chaperone-mediated protein complex assembly / MAP kinase kinase kinase activity / HSF1 activation / Attenuation phase / type II interferon-mediated signaling pathway / RHOBTB2 GTPase cycle / protein targeting / Purinergic signaling in leishmaniasis infection / cellular response to interleukin-4 / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / axonal growth cone / Schwann cell development / DNA polymerase binding / supramolecular fiber organization / chaperone-mediated protein folding / Signaling by ERBB2 / heat shock protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to muscle stretch / nitric-oxide synthase regulator activity / myelination / protein dephosphorylation / CD209 (DC-SIGN) signaling / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / : / insulin-like growth factor receptor signaling pathway Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Jaime-Garza, M. / Nowotny, C.A. / Coutandin, D. / Wang, F. / Tabios, M. / Agard, D.A. | |||||||||||||||
Funding support | United States, 4items
| |||||||||||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Hsp90 provides a platform for kinase dephosphorylation by PP5. Authors: Maru Jaime-Garza / Carlos A Nowotny / Daniel Coutandin / Feng Wang / Mariano Tabios / David A Agard / Abstract: The Hsp90 molecular chaperone collaborates with the phosphorylated Cdc37 cochaperone for the folding and activation of its many client kinases. As with many kinases, the Hsp90 client kinase CRaf is ...The Hsp90 molecular chaperone collaborates with the phosphorylated Cdc37 cochaperone for the folding and activation of its many client kinases. As with many kinases, the Hsp90 client kinase CRaf is activated by phosphorylation at specific regulatory sites. The cochaperone phosphatase PP5 dephosphorylates CRaf and Cdc37 in an Hsp90-dependent manner. Although dephosphorylating Cdc37 has been proposed as a mechanism for releasing Hsp90-bound kinases, here we show that Hsp90 bound kinases sterically inhibit Cdc37 dephosphorylation indicating kinase release must occur before Cdc37 dephosphorylation. Our cryo-EM structure of PP5 in complex with Hsp90:Cdc37:CRaf reveals how Hsp90 both activates PP5 and scaffolds its association with the bound CRaf to dephosphorylate phosphorylation sites neighboring the kinase domain. Thus, we directly show how Hsp90's role in maintaining protein homeostasis goes beyond folding and activation to include post translationally modifying its client kinases. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gae.cif.gz | 740.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gae.ent.gz | 614.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gae_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8gae_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8gae_validation.xml.gz | 70.6 KB | Display | |
Data in CIF | 8gae_validation.cif.gz | 106.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/8gae ftp://data.pdbj.org/pub/pdb/validation_reports/ga/8gae | HTTPS FTP |
-Related structure data
Related structure data | 29895MC 8gftC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 83595.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sequence starts with HRV 3C cleavage site, followed by human Hsp90B sequence. Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPCB / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): JEL-1 / References: UniProt: P08238 #2: Protein | | Mass: 45352.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC37, CDC37A / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): JEL-1 / References: UniProt: Q16543 #3: Protein | | Mass: 23841.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): JEL-1 References: UniProt: P04049, non-specific serine/threonine protein kinase #4: Protein | | Mass: 57184.730 Da / Num. of mol.: 1 / Mutation: H304A Source method: isolated from a genetically manipulated source Details: Sequence starts with HRV 3C cleavage site, continued by human PP5 sequence. Source: (gene. exp.) Homo sapiens (human) / Gene: PPP5C, PPP5 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P53041, protein-serine/threonine phosphatase |
---|
-Non-polymers , 5 types, 8 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ADP / | #8: Chemical | ChemComp-ATP / | #9: Chemical | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight |
| ||||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K Details: 3UL OF SAMPLE 10C 100% HUMIDITY 30S WAIT TIME 3S BLOT TIME -2 BLOT FORCE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 69 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 4160 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3730385 / Details: Gaussian blob particle picking in cryoSPARC. | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 522000 / Algorithm: FOURIER SPACE Details: Three different maps were used for final composite map: Hsp90:Cdc37: 288k particles, 3.2A PP5 TPR: 215k particles, 3.3A PP5 catalytic domain and CRaf kinase C-lobe: 22k particles, 4.0A ...Details: Three different maps were used for final composite map: Hsp90:Cdc37: 288k particles, 3.2A PP5 TPR: 215k particles, 3.3A PP5 catalytic domain and CRaf kinase C-lobe: 22k particles, 4.0A Composite half maps were used to get the final resolution in Relion PostProcessing. All original maps provided in the "Related entries" tab. Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT Details: This model was built using rigid body docking in Chimera and ChimeraX for all main chains, and RosettaCM to add remaining fragments not included in previous models. Refinement was done using ...Details: This model was built using rigid body docking in Chimera and ChimeraX for all main chains, and RosettaCM to add remaining fragments not included in previous models. Refinement was done using iterative Phenix and RosettaRelax, and finalized with ISOLDE. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.3 Å |