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- PDB-6n8z: HSP104DWB extended conformation -

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Basic information

Entry
Database: PDB / ID: 6n8z
TitleHSP104DWB extended conformation
ComponentsHeat shock protein 104Heat shock response
KeywordsCHAPERONE / Hsp104 / ClpB / protein disaggregase / molecular chaperone / AAA+ / ATPase / cryo-EM
Function / homologyAAA lid domain / ClpA/B family / Chaperonins clpA/B signature 2. / Chaperonins clpA/B signature 1. / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Clp amino terminal domain, pathogenicity island component / ATPase family associated with various cellular activities (AAA) / Clp, N-terminal domain superfamily / ClpA/B, conserved site 2 ...AAA lid domain / ClpA/B family / Chaperonins clpA/B signature 2. / Chaperonins clpA/B signature 1. / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Clp amino terminal domain, pathogenicity island component / ATPase family associated with various cellular activities (AAA) / Clp, N-terminal domain superfamily / ClpA/B, conserved site 2 / P-loop containing nucleoside triphosphate hydrolase / Clp ATPase, C-terminal / ClpA/B, conserved site 1 / Clp, N-terminal / ATPase, AAA-type, core / AAA+ ATPase domain / inheritance of oxidatively modified proteins involved in replicative cell aging / trehalose metabolism in response to heat stress / TRC complex / cellular heat acclimation / protein folding in endoplasmic reticulum / stress granule disassembly / protein metabolic process / chaperone cofactor-dependent protein refolding / protein unfolding / nuclear periphery / ADP binding / ATPase activity, coupled / unfolded protein binding / chaperone binding / ATP binding / identical protein binding / nucleus / cytoplasm / Heat shock protein 104
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9.3 Å resolution
AuthorsLee, S. / Rho, S.H. / Lee, J. / Sung, N. / Liu, J. / Tsai, F.T.F.
CitationJournal: Cell Rep / Year: 2019
Title: Cryo-EM Structures of the Hsp104 Protein Disaggregase Captured in the ATP Conformation.
Authors: Sukyeong Lee / Soung Hun Roh / Jungsoon Lee / Nuri Sung / Jun Liu / Francis T F Tsai
Abstract: Hsp104 is a ring-forming, ATP-driven molecular machine that recovers functional protein from both stress-denatured and amyloid-forming aggregates. Although Hsp104 shares a common architecture with ...Hsp104 is a ring-forming, ATP-driven molecular machine that recovers functional protein from both stress-denatured and amyloid-forming aggregates. Although Hsp104 shares a common architecture with Clp/Hsp100 protein unfoldases, different and seemingly conflicting 3D structures have been reported. Examining the structure of Hsp104 poses considerable challenges because Hsp104 readily hydrolyzes ATP, whereas ATP analogs can be slowly turned over and are often contaminated with other nucleotide species. Here, we present the single-particle electron cryo-microscopy (cryo-EM) structures of a catalytically inactive Hsp104 variant (Hsp104) in the ATP-bound state determined between 7.7 Å and 9.3 Å resolution. Surprisingly, we observe that the Hsp104 hexamer adopts distinct ring conformations (closed, extended, and open) despite being in the same nucleotide state. The latter underscores the structural plasticity of Hsp104 in solution, with different conformations stabilized by nucleotide binding. Our findings suggest that, in addition to ATP hydrolysis-driven conformational changes, Hsp104 uses stochastic motions to translocate unfolded polypeptides.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 30, 2018 / Release: Jan 2, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 2, 2019Structure modelrepositoryInitial release
1.1Jan 16, 2019Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Assembly

Deposited unit
A: Heat shock protein 104
B: Heat shock protein 104
C: Heat shock protein 104
D: Heat shock protein 104
E: Heat shock protein 104
F: Heat shock protein 104
hetero molecules


Theoretical massNumber of molelcules
Total (without water)600,36718
Polyers594,2816
Non-polymers6,08612
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)50060
ΔGint (kcal/M)-44
Surface area (Å2)160890

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Components

#1: Protein/peptide
Heat shock protein 104 / Heat shock response / Protein aggregation-remodeling factor HSP104


Mass: 99046.859 Da / Num. of mol.: 6
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HSP104, YLL026W, L0948 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: P31539
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

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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: Hexamer of Hsp104 with ATP / Type: COMPLEX / Details: Hsp 104 double Walker B mutant / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.6 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionDetails: Buffer solution is freshly prepared. / pH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
150 mMMOPSC7H15NO4S1
210 mMMagnesium ChlorideMgCl21
35 mMATPC10H16N5O13P31
SpecimenConc.: 0.3 mg/ml / Details: This sample was mono disperse. / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 kelvins / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 7.6 sec. / Electron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 1394

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 33666 / Symmetry type: POINT

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