+Open data
-Basic information
Entry | Database: PDB / ID: 7z38 | |||||||||||||||
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Title | Structure of the RAF1-HSP90-CDC37 complex (RHC-I) | |||||||||||||||
Components |
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Keywords | TRANSFERASE / RAF1-HSP90-CDC37 / complex / proto-oncogene / serine/threonine kinase / cancer / chaperone | |||||||||||||||
Function / homology | Function and homology information regulation of type II interferon-mediated signaling pathway / receptor ligand inhibitor activity / HSP90-CDC37 chaperone complex / death-inducing signaling complex assembly / positive regulation of mitophagy in response to mitochondrial depolarization / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / intermediate filament cytoskeleton organization / dynein axonemal particle ...regulation of type II interferon-mediated signaling pathway / receptor ligand inhibitor activity / HSP90-CDC37 chaperone complex / death-inducing signaling complex assembly / positive regulation of mitophagy in response to mitochondrial depolarization / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / intermediate filament cytoskeleton organization / dynein axonemal particle / histone methyltransferase binding / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of protein localization to cell surface / Rap1 signalling / ATP-dependent protein binding / regulation of cell motility / insulin secretion involved in cellular response to glucose stimulus / protein kinase regulator activity / protein folding chaperone complex / MAP kinase kinase kinase activity / 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 / IFNG signaling activates MAPKs / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / TPR domain binding / ERBB2-ERBB3 signaling pathway / regulation of cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / Assembly and release of respiratory syncytial virus (RSV) virions / face development / pseudopodium / dendritic growth cone / somatic stem cell population maintenance / regulation of type I interferon-mediated signaling pathway / : / thyroid gland development / neurotrophin TRK receptor signaling pathway / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / The NLRP3 inflammasome / Signaling by ERBB2 / telomere maintenance via telomerase / HSF1-dependent transactivation / response to unfolded protein / extrinsic apoptotic signaling pathway via death domain receptors / chaperone-mediated protein complex assembly / HSF1 activation / Attenuation phase / protein targeting / cellular response to interleukin-4 / negative regulation of protein-containing complex assembly / RHOBTB2 GTPase cycle / axonal growth cone / Purinergic signaling in leishmaniasis infection / Schwann cell development / type II interferon-mediated signaling pathway / activation of adenylate cyclase activity / DNA polymerase binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / supramolecular fiber organization / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding chaperone / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to muscle stretch / nitric-oxide synthase regulator activity / myelination / CD209 (DC-SIGN) signaling / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / insulin-like growth factor receptor signaling pathway / Signaling by ERBB2 TMD/JMD mutants / thymus development / peptide binding / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / placenta development / positive regulation of cell differentiation / ATP-dependent protein folding chaperone / kinase binding Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||||||||
Authors | Mesa, P. / Garcia-Alonso, S. / Barbacid, M. / Montoya, G. | |||||||||||||||
Funding support | Denmark, 4items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structure of the RAF1-HSP90-CDC37 complex reveals the basis of RAF1 regulation. Authors: Sara García-Alonso / Pablo Mesa / Laura de la Puente Ovejero / Gonzalo Aizpurua / Carmen G Lechuga / Eduardo Zarzuela / Clara M Santiveri / Manuel Sanclemente / Javier Muñoz / Mónica ...Authors: Sara García-Alonso / Pablo Mesa / Laura de la Puente Ovejero / Gonzalo Aizpurua / Carmen G Lechuga / Eduardo Zarzuela / Clara M Santiveri / Manuel Sanclemente / Javier Muñoz / Mónica Musteanu / Ramón Campos-Olivas / Jorge Martínez-Torrecuadrada / Mariano Barbacid / Guillermo Montoya / Abstract: RAF kinases are RAS-activated enzymes that initiate signaling through the MAPK cascade to control cellular proliferation, differentiation, and survival. Here, we describe the structure of the full- ...RAF kinases are RAS-activated enzymes that initiate signaling through the MAPK cascade to control cellular proliferation, differentiation, and survival. Here, we describe the structure of the full-length RAF1 protein in complex with HSP90 and CDC37 obtained by cryoelectron microscopy. The reconstruction reveals a RAF1 kinase with an unfolded N-lobe separated from its C-lobe. The hydrophobic core of the N-lobe is trapped in the HSP90 dimer, while CDC37 wraps around the chaperone and interacts with the N- and C-lobes of the kinase. The structure indicates how CDC37 can discriminate between the different members of the RAF family. Our structural analysis also reveals that the folded RAF1 assembles with 14-3-3 dimers, suggesting that after folding RAF1 follows a similar activation as B-RAF. Finally, disruption of the interaction between CDC37 and the DFG segment of RAF1 unveils potential vulnerabilities in attempting the pharmacological degradation of RAF1 for therapeutic purposes. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z38.cif.gz | 452.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z38.ent.gz | 292.2 KB | Display | PDB format |
PDBx/mmJSON format | 7z38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z38_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7z38_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7z38_validation.xml.gz | 61.1 KB | Display | |
Data in CIF | 7z38_validation.cif.gz | 86.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/7z38 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/7z38 | HTTPS FTP |
-Related structure data
Related structure data | 14473MC 7z37C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 84371.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal HA-tag + HSP90-beta / Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPCB / Plasmid: pcDNA3 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P08238 #2: Protein | | Mass: 74409.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: RAF1 + linker Gly-Ser-Ala + C-terminal StrepTagII / Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Plasmid: pcDNA3 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) References: UniProt: P04049, non-specific serine/threonine protein kinase #3: Protein | | Mass: 46535.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CDC37 + C-terminal Myc-DDK tag / Source: (gene. exp.) Homo sapiens (human) / Gene: CDC37, CDC37A / Plasmid: pCMV6 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q16543 #4: Chemical | #5: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RAF1-HSP90-CDC37 complex, RHC-I / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.28913380 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: Expi293F cells | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 3 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8138 Details: 8138 images (4430 non-tilted and 3708 30 degrees tilted) |
Image scans | Width: 4096 / Height: 4096 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3760000 Details: 3760k in total: 1353k RAF1:HSP90:CDC37 complex, 1127k 14-3-3 dimer, RAF1:14-3-3 complex 1245k | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266000 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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