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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3342 | |||||||||
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Title | Atomic cryoEM structure of Hsp90/Cdc37/Cdk4 complex | |||||||||
![]() | Reconstruction of Hsp90:Cdc37:Cdk4 complex. Part of series of maps, the highest resolution map being EMD-3337. This is a different subclass from the same particles as in EMD-3337, having well defined Cdk4 N-Lobe. Other relevant maps are EMD-3338, EMD-3339, EMD-3340, EMD-3341 | |||||||||
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![]() | Hsp90 / Cdc37 / Cdk4 / chaperone / kinase / unfolding | |||||||||
Function / homology | ![]() 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 / Drug-mediated inhibition of CDK4/CDK6 activity / regulation of type II interferon-mediated signaling pathway ...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 / Drug-mediated inhibition of CDK4/CDK6 activity / regulation of type II interferon-mediated signaling pathway / 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 / receptor ligand inhibitor activity / PTK6 Regulates Cell Cycle / very long-chain fatty acid metabolic process / HSP90-CDC37 chaperone complex / positive regulation of mitophagy in response to mitochondrial depolarization / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / cellular response to phorbol 13-acetate 12-myristate / Transcriptional regulation by RUNX2 / mitochondrial genome maintenance / positive regulation of protein localization to cell surface / ATP-dependent protein binding / cyclin-dependent kinase / protein kinase regulator activity / cyclin-dependent protein serine/threonine kinase activity / protein folding chaperone complex / cyclin-dependent protein serine/threonine kinase regulator activity / post-transcriptional regulation of gene expression / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of G2/M transition of mitotic cell cycle / 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 / positive regulation of transforming growth factor beta receptor signaling pathway / Assembly and release of respiratory syncytial virus (RSV) virions / cyclin-dependent protein kinase holoenzyme complex / regulation of G2/M transition of mitotic cell cycle / dendritic growth cone / regulation of type I interferon-mediated signaling pathway / : / : / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / The NLRP3 inflammasome / Signaling by ERBB2 / telomere maintenance via telomerase / HSF1-dependent transactivation / cyclin binding / response to unfolded protein / chaperone-mediated protein complex assembly / HSF1 activation / bicellular tight junction / Attenuation phase / protein targeting / cellular response to interleukin-4 / RHOBTB2 GTPase cycle / axonal growth cone / Purinergic signaling in leishmaniasis infection / DNA polymerase binding / 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 / nitric-oxide synthase regulator activity / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / Signaling by ERBB2 TMD/JMD mutants / Meiotic recombination / peptide binding / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Ubiquitin-dependent degradation of Cyclin D / Signaling by ERBB2 KD Mutants / placenta development / positive regulation of cell differentiation / Transcriptional regulation of granulopoiesis / SCF(Skp2)-mediated degradation of p27/p21 / ATP-dependent protein folding chaperone / kinase binding / Downregulation of ERBB2 signaling Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
![]() | Verba KA / Wang RYR / Arakawa A / Liu Y / Shirouzu M / Yokoyama S / Agard DA | |||||||||
![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17 KB 17 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 128.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fwmMC ![]() 3337C ![]() 3338C ![]() 3339C ![]() 3340C ![]() 3341C ![]() 3343C ![]() 3344C ![]() 5fwkC ![]() 5fwlC ![]() 5fwpC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of Hsp90:Cdc37:Cdk4 complex. Part of series of maps, the highest resolution map being EMD-3337. This is a different subclass from the same particles as in EMD-3337, having well defined Cdk4 N-Lobe. Other relevant maps are EMD-3338, EMD-3339, EMD-3340, EMD-3341 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.315 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Complex of Human Hsp90 beta, human Cdc37 and human Cdk4
Entire | Name: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4 |
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Components |
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-Supramolecule #1000: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4
Supramolecule | Name: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4 type: sample / ID: 1000 / Details: All three proteins were co-expressed in Sf9 cells. Oligomeric state: One Hsp90 homodimer binds to one Cdc37 and one Cdk4 Number unique components: 3 |
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Molecular weight | Experimental: 245 KDa / Theoretical: 245 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: ![]() |
Molecular weight | Theoretical: 83 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() |
Molecular weight | Theoretical: 44.5 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.7 KDa |
Recombinant expression | Organism: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.27 mg/mL |
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Buffer | pH: 7.5 Details: 20mM Tris-HCl (pH 7.5), 150 mM NaCl, 10 mM KCl, 10 mM MgCl2, 20 mM Na2MoO4, 2mM 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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: At high mag via FT. |
Date | Nov 25, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 3718 / Average electron dose: 44 e/Å2 / Details: 38 frames, 7.6 seconds total exposure / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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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, Rosetta |
Details | Residues 5-85 (N-lobe) of Cdk4 from 3G33 were fit in Chimera as rigid body into EMD-3342. Such fit N-lobe of Cdk4 was further tweaked in Coot in the context of 5FWK to join the Cdk4 chain and minimize clashes for each of the maps. To relieve atomic clashes or bond length/angle distortions at the linker regions, these models were subjected to "Cartesian space relax" protocol within corresponding density maps using Rosetta. Final models were selected using the combined score of Rosetta all-atom physically-realistic score and electron density score. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 130 Target criteria: cross correlation of fit into the density with Rosetta force field score |
Output model | ![]() PDB-5fwm: |