+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3344 | |||||||||
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Title | Atomic cryoEM structure of Hsp90/Cdc37/Cdk4 complex | |||||||||
Map data | Reconstruction of Hsp90:Cdc37:Cdk4 complex. Cdk4 is tagged at the C terminus with T4 lysozyme. Part of series of maps, the highest resolution map being EMD-3337, others being EMD-3338, EMD-3339, EMD-3340, EMD-3341, EMD-3342, EMD-3343. | |||||||||
Sample |
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Keywords | Hsp90 / Cdc37 / Cdk4 / chaperone / kinase / unfolding | |||||||||
Function / homology | Function and homology information cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / cellular response to ionomycin / citrulline metabolic process / regulation of transcription initiation by RNA polymerase II / regulation of type II interferon-mediated signaling pathway / Drug-mediated inhibition of CDK4/CDK6 activity ...cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / cellular response to ionomycin / citrulline metabolic process / regulation of transcription initiation by RNA polymerase II / regulation of type II interferon-mediated signaling pathway / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / regulation of type B pancreatic cell proliferation / : / very long-chain fatty acid metabolic process / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / positive regulation of mitophagy in response to mitochondrial depolarization / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex / histone methyltransferase binding / Transcriptional regulation by RUNX2 / cellular response to phorbol 13-acetate 12-myristate / mitochondrial genome maintenance / protein kinase regulator activity / positive regulation of protein localization to cell surface / ATP-dependent protein binding / protein folding chaperone complex / negative regulation of protein metabolic process / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of tau-protein kinase activity / post-transcriptional regulation of gene expression / telomerase holoenzyme complex assembly / Uptake and function of diphtheria toxin / 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 / PTK6 Regulates Cell Cycle / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / dendritic growth cone / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / regulation of type I interferon-mediated signaling pathway / positive regulation of phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / telomere maintenance via telomerase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / response to unfolded protein / bicellular tight junction / cyclin-dependent protein kinase holoenzyme complex / protein targeting / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / cyclin-dependent kinase / RHOBTB2 GTPase cycle / cyclin-dependent protein serine/threonine kinase activity / DNA polymerase binding / Purinergic signaling in leishmaniasis infection / supramolecular fiber organization / axonal growth cone / Signaling by ERBB2 / positive regulation of telomerase activity / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of G2/M transition of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cellular response to interleukin-4 / nitric-oxide synthase regulator activity / cyclin binding / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / placenta development / response to organic substance / Ubiquitin-dependent degradation of Cyclin D / positive regulation of cell differentiation / peptide binding / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / Hsp90 protein binding / G1/S transition of mitotic cell cycle / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Oncogene Induced Senescence / Signaling by ERBB2 KD Mutants Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Verba KA / Wang RYR / Arakawa A / Liu Y / Shirouzu M / Yokoyama S / Agard DA | |||||||||
Citation | Journal: Science / Year: 2016 Title: Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase. Authors: Kliment A Verba / Ray Yu-Ruei Wang / Akihiko Arakawa / Yanxin Liu / Mikako Shirouzu / Shigeyuki Yokoyama / David A Agard / Abstract: The Hsp90 molecular chaperone and its Cdc37 cochaperone help stabilize and activate more than half of the human kinome. However, both the mechanism by which these chaperones assist their "client" ...The Hsp90 molecular chaperone and its Cdc37 cochaperone help stabilize and activate more than half of the human kinome. However, both the mechanism by which these chaperones assist their "client" kinases and the reason why some kinases are addicted to Hsp90 while closely related family members are independent are unknown. Our structural understanding of these interactions is lacking, as no full-length structures of human Hsp90, Cdc37, or either of these proteins with a kinase have been elucidated. Here we report a 3.9 angstrom cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex. Surprisingly, the two lobes of Cdk4 are completely separated with the β4-β5 sheet unfolded. Cdc37 mimics part of the kinase N lobe, stabilizing an open kinase conformation by wedging itself between the two lobes. Finally, Hsp90 clamps around the unfolded kinase β5 strand and interacts with exposed N- and C-lobe interfaces, protecting the kinase in a trapped unfolded state. On the basis of this structure and an extensive amount of previously collected data, we propose unifying conceptual and mechanistic models of chaperone-kinase interactions. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3344.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-3344-v30.xml emd-3344.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3344_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_3344.tif | 115.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3344 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3344 | HTTPS FTP |
-Related structure data
Related structure data | 3337C 3338C 3339C 3340C 3341C 3342C 3343C 5fwkC 5fwlC 5fwmC 5fwpC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3344.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Hsp90:Cdc37:Cdk4 complex. Cdk4 is tagged at the C terminus with T4 lysozyme. Part of series of maps, the highest resolution map being EMD-3337, others being EMD-3338, EMD-3339, EMD-3340, EMD-3341, EMD-3342, EMD-3343. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of Human Hsp90 beta, human Cdc37 and human Cdk4-T4 lysozyme
Entire | Name: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4-T4 lysozyme |
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Components |
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-Supramolecule #1000: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4-T4 lysozyme
Supramolecule | Name: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4-T4 lysozyme type: sample / ID: 1000 Details: All three proteins were co-expressed in Saccharomyces cerevisiae cells. Oligomeric state: One Hsp90 homodimer binds to one Cdc37 and one Cdk4-T4 Lysozyme Number unique components: 3 |
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Molecular weight | Experimental: 260 KDa / Theoretical: 260 KDa / Method: As cloned, verified by SDS-PAGE |
-Macromolecule #1: Heat Shock Protein HSP 90 beta
Macromolecule | Name: Heat Shock Protein HSP 90 beta / type: protein_or_peptide / ID: 1 / Name.synonym: Hsp90 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: cytoplasm |
Molecular weight | Theoretical: 83 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: 83nu |
Sequence | UniProtKB: Heat shock protein HSP 90-beta / GO: citrulline metabolic process / InterPro: Heat shock protein Hsp90 family |
-Macromolecule #2: Hsp90 co-chaperone Cdc37
Macromolecule | Name: Hsp90 co-chaperone Cdc37 / type: protein_or_peptide / ID: 2 / Name.synonym: Cdc37 / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: throughout |
Molecular weight | Theoretical: 44.5 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: 83nu |
Sequence | UniProtKB: Hsp90 co-chaperone Cdc37 / GO: mitochondrial genome maintenance |
-Macromolecule #3: Cyclin-dependent kinase 4
Macromolecule | Name: Cyclin-dependent kinase 4 / type: protein_or_peptide / ID: 3 / Name.synonym: Cdk4 Details: T4 lysozyme was fused recombinantly at the C terminus of Cdk4, with a GS linker in between. This was done to verify placement of proteins in the complex. Therefore, the total mass of Cdk4- ...Details: T4 lysozyme was fused recombinantly at the C terminus of Cdk4, with a GS linker in between. This was done to verify placement of proteins in the complex. Therefore, the total mass of Cdk4-T4Lys is 51kDa rather that 33.7kDa for pure Cdk4. Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: throughout |
Molecular weight | Theoretical: 33.7 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: 83nu |
Sequence | UniProtKB: Cyclin-dependent kinase 4 / GO: very long-chain fatty acid metabolic process / InterPro: Protein kinase domain |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.27 mg/mL |
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Buffer | pH: 7.5 Details: 20mM Tris pH 7.5, 150mM NaCl, 10mM KCl, 20mM NaMoO4, 1mM DTT, 0.085mM DDM |
Grid | Details: Glow discharged for 30 sec, C-flat 400 mesh 1.2/1.3 thick carbon grids (Protochips) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 95 K / Instrument: FEI VITROBOT MARK III / Method: Single blot from 4 to 6 seconds, at 20C |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 31000 |
Sample stage | Specimen holder: Polara 6 cartridge loader / Specimen holder model: OTHER |
Alignment procedure | Legacy - Astigmatism: At high mag via FT. |
Date | Sep 25, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1082 / Average electron dose: 40 e/Å2 / Details: 30 frames, 6 seconds total exposure / Bits/pixel: 8 |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: E / Chain - #3 - Chain ID: K |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |