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- PDB-6ahf: CryoEM Reconstruction of Hsp104 N728A Hexamer -

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Basic information

Entry
Database: PDB / ID: 6ahf
TitleCryoEM Reconstruction of Hsp104 N728A Hexamer
ComponentsHeat shock protein 104Heat shock response
KeywordsCHAPERONE / chaperone / Hsp / holdase
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 S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.78 Å resolution
AuthorsZhang, X. / Zhang, L. / Zhang, S.
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Heat shock protein 104 (HSP104) chaperones soluble Tau via a mechanism distinct from its disaggregase activity.
Authors: Xiang Zhang / Shengnan Zhang / Li Zhang / Jinxia Lu / Chunyu Zhao / Feng Luo / Dan Li / Xueming Li / Cong Liu
Abstract: Heat shock protein 104 (HSP104) is a conserved AAA+ protein disaggregase, can disassemble the toxic aggregates formed by different amyloid proteins, and is protective in various animal models ...Heat shock protein 104 (HSP104) is a conserved AAA+ protein disaggregase, can disassemble the toxic aggregates formed by different amyloid proteins, and is protective in various animal models associated with amyloid-related diseases. Extensive studies have attempted to elucidate how HSP104 disassembles the aggregated form of clients. Here, we found that HSP104 exhibits a potent holdase activity that does not require energy, prevents the soluble form of amyloid clients from aggregating, and differs from HSP104's disaggregase activity. Using cryo-EM, NMR and additional biophysical approaches, we found that HSP104 utilizes its small subdomain of nucleotide-binding domain 2 (ssNBD2) to capture the soluble amyloid client (K19 of Tau) independent of its ATP hydrolysis activity. Our results indicate that HSP104 utilizes two fundamental distinct mechanisms to chaperone different forms of amyloid client and highlight the important yet previously unappreciated function of ssNBD2 in chaperoning amyloid client and thereby preventing pathological aggregation.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 17, 2018 / Release: Feb 13, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 13, 2019Structure modelrepositoryInitial release
1.1Feb 20, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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)615,92512
Polyers612,7866
Non-polymers3,1396
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)20300
ΔGint (kcal/M)-70
Surface area (Å2)229730

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Components

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


Mass: 102130.938 Da / Num. of mol.: 6 / Mutation: N728A / Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: HSP104 / Production host: Escherichia coli (E. coli) / References: UniProt: P31539
#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 6 / Formula: C10H16N5O12P3S
Comment: ATP-gamma-S (energy-carrying molecule analogue) *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: CryoEM Reconstruction of Hsp104 N728A Hexamer / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 69537 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01732491
ELECTRON MICROSCOPYf_angle_d1.90843595
ELECTRON MICROSCOPYf_dihedral_angle_d11.23526900
ELECTRON MICROSCOPYf_chiral_restr0.0864772
ELECTRON MICROSCOPYf_plane_restr0.0105815

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