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

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Basic information

Entry
Database: EMDB / ID: EMD-9625
TitleCryoEM Reconstruction of Hsp104 N728A Hexamer
Map dataHsp104 N728A
Sample
  • Complex: CryoEM Reconstruction of Hsp104 N728A Hexamer
    • Protein or peptide: Heat shock protein 104
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Keywordschaperone / Hsp / holdase
Function / homology
Function and homology information


trehalose metabolism in response to heat stress / TRC complex / cellular heat acclimation / protein folding in endoplasmic reticulum / post-translational protein targeting to endoplasmic reticulum membrane / stress granule disassembly / chaperone cofactor-dependent protein refolding / protein unfolding / nuclear periphery / ADP binding ...trehalose metabolism in response to heat stress / TRC complex / cellular heat acclimation / protein folding in endoplasmic reticulum / post-translational protein targeting to endoplasmic reticulum membrane / stress granule disassembly / chaperone cofactor-dependent protein refolding / protein unfolding / nuclear periphery / ADP binding / unfolded protein binding / protein-folding chaperone binding / cellular response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. ...ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Heat shock protein 104
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.78 Å
AuthorsZhang X / Zhang L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470748 China
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.
History
DepositionAug 17, 2018-
Header (metadata) releaseFeb 13, 2019-
Map releaseFeb 13, 2019-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9625.png

Downloads & links

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Map

FileDownload / File: emd_9625.map.gz / Format: CCP4 / Size: 4.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHsp104 N728A
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.22324839 - 0.5061682
Average (Standard dev.)0.00023829518 (±0.023758441)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions108108108
Spacing108108108
CellA=B=C: 285.12003 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ300300300
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

Histogram

Histogram (log scale)

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Half map: EM half map of Hsp104 N728A

Fileemd_9625_half_map_1.map
AnnotationEM half map of Hsp104 N728A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map of Hsp104 N728A

Fileemd_9625_half_map_2.map
AnnotationEM half map of Hsp104 N728A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM Reconstruction of Hsp104 N728A Hexamer

EntireName: CryoEM Reconstruction of Hsp104 N728A Hexamer
Components
  • Complex: CryoEM Reconstruction of Hsp104 N728A Hexamer
    • Protein or peptide: Heat shock protein 104
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: CryoEM Reconstruction of Hsp104 N728A Hexamer

SupramoleculeName: CryoEM Reconstruction of Hsp104 N728A Hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

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Macromolecule #1: Heat shock protein 104

MacromoleculeName: Heat shock protein 104 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Molecular weightTheoretical: 102.130938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNDQTQFTER ALTILTLAQK LASDHQHPQL QPIHILAAFI ETPEDGSVPY LQNLIEKGRY DYDLFKKVVN RNLVRIPQQQ PAPAEITPS YALGKVLQDA AKIQKQQKDS FIAQDHILFA LFNDSSIQQI FKEAQVDIEA IKQQALELRG NTRIDSRGAD T NTPLEYLS ...String:
MNDQTQFTER ALTILTLAQK LASDHQHPQL QPIHILAAFI ETPEDGSVPY LQNLIEKGRY DYDLFKKVVN RNLVRIPQQQ PAPAEITPS YALGKVLQDA AKIQKQQKDS FIAQDHILFA LFNDSSIQQI FKEAQVDIEA IKQQALELRG NTRIDSRGAD T NTPLEYLS KYAIDMTEQA RQGKLDPVIG REEEIRSTIR VLARRIKSNP CLIGEPGIGK TAIIEGVAQR IIDDDVPTIL QG AKLFSLD LAALTAGAKY KGDFEERFKG VLKEIEESKT LIVLFIDEIH MLMGNGKDDA ANILKPALSR GQLKVIGATT NNE YRSIVE KDGAFERRFQ KIEVAEPSVR QTVAILRGLQ PKYEIHHGVR ILDSALVTAA QLAKRYLPYR RLPDSALDLV DISC AGVAV ARDSKPEELD SKERQLQLIQ VEIKALERDE DADSTTKDRL KLARQKEASL QEELEPLRQR YNEEKHGHEE LTQAK KKLD ELENKALDAE RRYDTATAAD LRYFAIPDIK KQIEKLEDQV AEEERRAGAN SMIQNVVDSD TISETAARLT GIPVKK LSE SENEKLIHME RDLSSEVVGQ MDAIKAVSNA VRLSRSGLAN PRQPASFLFL GLSGSGKTEL AKKVAGFLFN DEDMMIR VD CSELSEKYAV SKLLGTTAGY VGYDEGGFLT NQLQYKPYSV LLFDEVEKAH PDVLTVMLQM LDDGRITSGQ GKTIDCSN C IVIMTSALGA EFINSQQGSK IQESTKNLVM GAVRQHFRPE FLNRISSIVI FNKLSRKAIH KIVDIRLKEI EERFEQNDK HYKLNLTQEA KDFLAKYGYS DDMGARPLNR LIQNEILNKL ALRILKNEIK DKETVNVVLK KGKSRDENVP EEAEECLEVL PNHEATIGA DTLGDDDNED SMEIDDDLD

UniProtKB: Heat shock protein 104

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Macromolecule #2: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 6 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69537
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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