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- PDB-5fwm: Atomic cryoEM structure of Hsp90-Cdc37-Cdk4 complex -

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Entry
Database: PDB / ID: 5fwm
TitleAtomic cryoEM structure of Hsp90-Cdc37-Cdk4 complex
Components
  • CYCLIN-DEPENDENT KINASE 4
  • HEAT SHOCK PROTEIN HSP 90 BETA
  • HSP90 CO-CHAPERONE CDC37
KeywordsCHAPERONE / HSP90 / CDC37 / CDK4 / KINASE / UNFOLDING
Function / homologyHeat shock protein Hsp90 family / Protein kinase domain / Regulation of actin dynamics for phagocytic cup formation / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Signaling by ERBB2 / Protein kinase domain profile. / Heat shock hsp90 proteins family signature. / Protein kinase domain / Protein kinases ATP-binding region signature. ...Heat shock protein Hsp90 family / Protein kinase domain / Regulation of actin dynamics for phagocytic cup formation / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Signaling by ERBB2 / Protein kinase domain profile. / Heat shock hsp90 proteins family signature. / Protein kinase domain / Protein kinases ATP-binding region signature. / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 N terminal kinase binding / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Hsp90 protein / Cdc37, Hsp90-binding domain superfamily / Senescence-Associated Secretory Phenotype (SASP) / HSP90, C-terminal domain / Histidine kinase/HSP90-like ATPase superfamily / Heat shock protein Hsp90, N-terminal / Ribosomal protein S5 domain 2-type fold / Heat shock protein Hsp90, conserved site / Protein kinase, ATP binding site / Cdc37, Hsp90 binding / Cdc37, C-terminal / Cdc37, N-terminal domain / Protein kinase-like domain superfamily / Serine/threonine-protein kinase, active site / Cdc37 / Histidine kinase/HSP90-like ATPase / Oxidative Stress Induced Senescence / Serine/Threonine protein kinases active-site signature. / PTK6 Regulates Cell Cycle / The NLRP3 inflammasome / The role of GTSE1 in G2/M progression after G2 checkpoint / Ubiquitin-dependent degradation of Cyclin D1 / Neutrophil degranulation / Constitutive Signaling by EGFRvIII / Downregulation of ERBB2 signaling / Transcriptional regulation by RUNX2 / Uptake and function of diphtheria toxin / Sema3A PAK dependent Axon repulsion / Aryl hydrocarbon receptor signalling / Transcriptional regulation of white adipocyte differentiation / HSF1-dependent transactivation / Attenuation phase / ESR-mediated signaling / HSF1 activation / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Estrogen-dependent gene expression / RMTs methylate histone arginines / Meiotic recombination / Oncogene Induced Senescence / Cyclin D associated events in G1 / HSP90-CDC37 chaperone complex / cellular response to phorbol 13-acetate 12-myristate / regulation of lipid biosynthetic process / negative regulation of transforming growth factor beta activation / ooplasm / cyclin D2-CDK4 complex / sperm head plasma membrane / sulfonylurea receptor binding / regulation of lipid catabolic process / aryl hydrocarbon receptor complex / positive regulation of cyclin-dependent protein kinase activity / dATP binding / CTP binding / positive regulation of mitophagy in response to mitochondrial depolarization / cellular response to ionomycin / negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle / negative regulation of proteasomal protein catabolic process / histone methyltransferase binding / negative regulation of protein metabolic process / negative regulation of complement-dependent cytotoxicity / ATP-dependent protein binding / UTP binding / cyclin-dependent protein serine/threonine kinase regulator activity / posttranscriptional regulation of gene expression / protein kinase regulator activity / positive regulation of protein localization to cell surface / regulation of insulin receptor signaling pathway / chaperone complex / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of cell size / supramolecular fiber organization / regulation of interferon-gamma-mediated signaling pathway / lens development in camera-type eye / response to salt stress / protein targeting / brush border membrane / regulation of cyclin-dependent protein serine/threonine kinase activity / adipose tissue development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of type I interferon-mediated signaling pathway / response to testosterone / telomerase holoenzyme complex assembly / positive regulation of phosphoprotein phosphatase activity / TPR domain binding / inclusion body / dendritic growth cone
Function and homology information
Specimen sourceHOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8 Å resolution
AuthorsVerba, K.A. / Wang, R.Y.R. / Arakawa, A. / Liu, Y. / Yokoyama, S. / Agard, D.A.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 18, 2016 / Release: Jul 6, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 6, 2016Structure modelrepositoryInitial release
1.1Apr 19, 2017Structure modelOther
1.2Aug 2, 2017Structure modelData collectionem_image_scans / em_software_em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-3342
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Structure viewerMolecule:
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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN HSP 90 BETA
B: HEAT SHOCK PROTEIN HSP 90 BETA
E: HSP90 CO-CHAPERONE CDC37
K: CYCLIN-DEPENDENT KINASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,4978
Polyers246,4344
Non-polymers1,0634
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein/peptide HEAT SHOCK PROTEIN HSP 90 BETA / / HSP 90 / HEAT SHOCK 84 KDA / HSP 84 / HSP84 / HEAT SHOCK PROTEIN HSP 90 BETA


Mass: 83645.539 Da / Num. of mol.: 2 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid name: PFASTBACHT / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P08238
#2: Protein/peptide HSP90 CO-CHAPERONE CDC37 / HSP90 CHAPERONE PROTEIN KINASE-TARGETING SUBUNIT / P50CDC37


Mass: 44622.363 Da / Num. of mol.: 1 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid name: PFASTBACHT / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q16543
#3: Protein/peptide CYCLIN-DEPENDENT KINASE 4 /


Mass: 34520.629 Da / Num. of mol.: 1 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid name: PFASTBACHT / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P11802
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: COMPLEX OF HUMAN HSP90BETA, HUMAN CDC37 AND HUMAN CDK4
Type: COMPLEX
Buffer solutionName: 20MM TRIS-HCL (PH 7.5), 150 MM NACL, 10 MM KCL, 10 MM MGCL2, 20 MM NA2MOO4, 2MM DTT, 0.085MM DDM
Details: 20MM TRIS-HCL (PH 7.5), 150 MM NACL, 10 MM KCL, 10 MM MGCL2, 20 MM NA2MOO4, 2MM DTT, 0.085MM DDM
pH: 7.5
SpecimenConc.: 0.27 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Nov 25, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Nominal defocus max: 3800 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1Rosettamodel fitting
2UCSF Chimeramodel fitting
3RELION3D reconstruction
SymmetryPoint symmetry: C1
3D reconstructionResolution: 8 Å / Number of particles: 61981 / Actual pixel size: 1.315
Details: THIS MODEL WAS BUILT BASED ON 5FWK WITH CDK4 N-LOBE RIGID BODY FIT INTO THE EM DENSITY. THE MODEL WAS THEN MINIMIZED IN ROSETTA. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3342. (DEPOSITION ID: 14285).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--ROSETTA / Ref protocol: OTHER
Least-squares processHighest resolution: 8 Å
Refine hist #LASTHighest resolution: 8 Å
Number of atoms included #LASTProtein: 14743 / Nucleic acid: 0 / Ligand: 64 / Solvent: 0 / Total: 14807

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