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- EMDB-9625: CryoEM Reconstruction of Hsp104 N728A Hexamer -

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Entry
Database: EMDB / ID: 9625
TitleCryoEM Reconstruction of Hsp104 N728A Hexamer
Map dataHsp104 N728A
SampleCryoEM Reconstruction of Hsp104 N728A Hexamer
  • Heat shock protein 104Heat shock response
  • ligand
Function / homologyClp, N-terminal domain superfamily / AAA+ ATPase domain / 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) / ClpA/B family / ClpA/B, conserved site 2 ...Clp, N-terminal domain superfamily / AAA+ ATPase domain / 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) / ClpA/B family / 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 / 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
SourceSaccharomyces cerevisiae S288c (yeast)
Methodsingle 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 ReportPDB-ID: 6ahf

SummaryFull reportAbout validation report
DateDeposition: Aug 17, 2018 / Header (metadata) release: Feb 13, 2019 / Map release: Feb 13, 2019 / Last update: Feb 20, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ahf
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9625.map.gz (map file in CCP4 format, 5039 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
108 pix
2.64 Å/pix.
= 285.12 Å
108 pix
2.64 Å/pix.
= 285.12 Å
108 pix
2.64 Å/pix.
= 285.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.64 Å
Density
Contour Level:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.08462056 (0.26067045)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions108108108
Origin0.00.00.0
Limit107.0107.0107.0
Spacing108108108
CellA=B=C: 285.12003 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.642.642.64
M x/y/z108108108
origin x/y/z0.0000.0000.000
length x/y/z285.120285.120285.120
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS108108108
D min/max/mean-0.2230.5060.000

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Supplemental data

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Mask #1

Fileemd_9625_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire CryoEM Reconstruction of Hsp104 N728A Hexamer

EntireName: CryoEM Reconstruction of Hsp104 N728A Hexamer / Number of components: 3

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Component #1: protein, CryoEM Reconstruction of Hsp104 N728A Hexamer

ProteinName: CryoEM Reconstruction of Hsp104 N728A Hexamer / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Heat shock protein 104

ProteinName: Heat shock protein 104Heat shock response / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 102.130938 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: ligand, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.523247 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: OTHER
LensImaging mode: OTHER
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 69537
3D reconstructionResolution: 6.78 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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