+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3341 | |||||||||
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Title | Atomic cryoEM structure of Hsp90/Cdc37/Cdk4 complex | |||||||||
Map data | 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. | |||||||||
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 / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 ...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 / 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 II interferon-mediated signaling pathway / regulation of type B pancreatic cell proliferation / hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / HSP90-CDC37 chaperone complex / receptor ligand inhibitor activity / very long-chain fatty acid metabolic process / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / : / Cellular response to hypoxia / aryl hydrocarbon receptor complex / dynein axonemal particle / carboxylic acid binding / histone methyltransferase binding / positive regulation of vasculogenesis / Transcriptional regulation by RUNX2 / cellular response to phorbol 13-acetate 12-myristate / mitochondrial genome maintenance / ankyrin repeat binding / ATP-dependent protein binding / positive regulation of protein localization to cell surface / protein kinase regulator activity / Notch binding / protein folding chaperone complex / oxygen sensor activity / cyclin-dependent protein serine/threonine kinase regulator activity / telomerase holoenzyme complex assembly / post-transcriptional regulation of gene expression / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / 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 / negative regulation of Notch signaling pathway / PTK6 Regulates Cell Cycle / Assembly and release of respiratory syncytial virus (RSV) virions / positive regulation of transforming growth factor beta receptor signaling pathway / dendritic growth cone / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / regulation of type I interferon-mediated signaling pathway / The NLRP3 inflammasome / : / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / telomere maintenance via telomerase / HSF1-dependent transactivation / response to unfolded protein / NF-kappaB binding / chaperone-mediated protein complex assembly / HSF1 activation / bicellular tight junction / Attenuation phase / positive regulation of myoblast differentiation / cyclin-dependent kinase / RHOBTB2 GTPase cycle / protein targeting / cyclin-dependent protein serine/threonine kinase activity / cellular response to interleukin-4 / Purinergic signaling in leishmaniasis infection / axonal growth cone / DNA polymerase binding / cyclin-dependent protein kinase holoenzyme complex / supramolecular fiber organization / chaperone-mediated protein folding / Signaling by ERBB2 / heat shock protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of G2/M transition of mitotic cell cycle / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of G2/M transition of mitotic cell cycle / nitric-oxide synthase regulator activity / cyclin binding / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / Ubiquitin-dependent degradation of Cyclin D Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 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_3341.map.gz | 60 MB | EMDB map data format | |
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Header (meta data) | emd-3341-v30.xml emd-3341.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3341_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_3341.tif | 135.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3341 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3341 | HTTPS FTP |
-Validation report
Summary document | emd_3341_validation.pdf.gz | 270.5 KB | Display | EMDB validaton report |
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Full document | emd_3341_full_validation.pdf.gz | 269.6 KB | Display | |
Data in XML | emd_3341_validation.xml.gz | 10.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3341 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3341 | HTTPS FTP |
-Related structure data
Related structure data | 5fwlMC 5jwlM 3337C 3338C 3339C 3340C 3342C 3343C 3344C 5fwkC 5fwmC 5fwpC M: atomic model generated by this map 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_3341.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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: Homo sapiens (human) / synonym: Human / Location in cell: cytoplasm |
Molecular weight | Theoretical: 83 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant plasmid: pFastBacHT |
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: Spodoptera frugiperda (fall armyworm) / Recombinant plasmid: pFastBacHT |
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: Homo sapiens (human) / synonym: Human / Location in cell: throughout |
Molecular weight | Theoretical: 33.7 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant plasmid: pFastBacHT |
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-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 |
-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: FIELD EMISSION GUN |
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 |
-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-3341. 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: 200 Target criteria: cross correlation of fit into the density with Rosetta force field score |
Output model | PDB-5fwl: PDB-5jwl: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: Chimera, Rosetta |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 200 Target criteria: cross correlation of fit into the density with Rosetta force field score |
Output model | PDB-5fwl: PDB-5jwl: |