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- EMDB-0375: Hsp104DWB closed conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-0375
TitleHsp104DWB closed conformation
Map dataHsp104DWB in closed conformation, primary map
Sample
  • Complex: Hexamer of Hsp104 with ATP
    • Protein or peptide: Heat shock protein 104
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsHsp104 / ClpB / protein disaggregase / molecular chaperone / AAA+ / ATPase / cryo-EM / CHAPERONE
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 (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsLee S / Rho SH
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.
History
DepositionNov 30, 2018-
Header (metadata) releaseJan 2, 2019-
Map releaseJan 2, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n8t
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0375.png

Downloads & links

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Map

FileDownload / File: emd_0375.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHsp104DWB in closed conformation, primary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 160 pix.
= 268.8 Å		1.68 Å/pix.
x 160 pix.
= 268.8 Å		1.68 Å/pix.
x 160 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.83835846 - 1.5057886
Average (Standard dev.)-0.00000000033869 (±0.106457874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.681.681.68
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800268.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.8381.506-0.000

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Supplemental data

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Sample components

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Entire : Hexamer of Hsp104 with ATP

EntireName: Hexamer of Hsp104 with ATP
Components
  • Complex: Hexamer of Hsp104 with ATP
    • Protein or peptide: Heat shock protein 104
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Hexamer of Hsp104 with ATP

SupramoleculeName: Hexamer of Hsp104 with ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Hsp 104 double Walker B mutant
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 600 KDa

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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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 99.046859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QFTERALTIL TLAQKLASDH QHPQLQPIHI LAAFIETPED GSVPYLQNLI EKGRYDYDLF KKVVNRNLVR IPQQQPAPAE ITPSYALGK VLQDAAKIQK QQKDSFIAQD HILFALFNDS SIQQIFKEAQ VDIEAIKQQA LELRGNTRID SRGADTNTPL E YLSKYAID ...String:
QFTERALTIL TLAQKLASDH QHPQLQPIHI LAAFIETPED GSVPYLQNLI EKGRYDYDLF KKVVNRNLVR IPQQQPAPAE ITPSYALGK VLQDAAKIQK QQKDSFIAQD HILFALFNDS SIQQIFKEAQ VDIEAIKQQA LELRGNTRID SRGADTNTPL E YLSKYAID MTEQARQGKL DPVIGREEEI RSTIRVLARR IKSNPCLIGE PGIGKTAIIE GVAQRIIDDD VPTILQGAKL FS LDLAALT AGAKYKGDFE ERFKGVLKEI EESKTLIVLF IDEIHMLMGN GKDDAANILK PALSRGQLKV IGATTNNEYR SIV EKDGAF ERRFQKIEVA EPSVRQTVAI LRGLQPKYEI HHGVRILDSA LVTAAQLAKR YLPYRRLPDS ALDLVDISCA GVAV ARDSK PEELDSKERQ LQLIQVEIKA LERDEDADST TKDRLKLARQ KEASLQEELE PLRQRYNEEK HGHEELTQAK KKLDE LENK ALDAERRYDT ATAADLRYFA IPDIKKQIEK LEDQVAEEER RAGANSMIQN VVDSDTISET AARLTGIPVK KLSESE NEK LIHMERDLSS EVVGQMDAIK AVSNAVRLSR SGLANPRQPA SFLFLGLSGS GKTELAKKVA GFLFNDEDMM IRVDCSE LS EKYAVSKLLG TTAGYVGYDE GGFLTNQLQY KPYSVLLFDE VEKAHPDVLT VMLQMLDDGR ITSGQGKTID CSNCIVIM T SNLGAEFINS QQGSKIQEST KNLVMGAVRQ HFRPEFLNRI SSIVIFNKLS RKAIHKIVDI RLKEIEERFE QNDKHYKLN LTQEAKDFLA KYGYSDDMGA RPLNRLIQNE ILNKLALRIL KNEIKDKETV NVVLKKGKSR DENVPEEAEE CLEVLPNHE

UniProtKB: Heat shock protein 104

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC7H15NO4SMOPS
10.0 mMMgCl2Magnesium Chloride
5.0 mMC10H16N5O13P3ATP

Details: Buffer solution is freshly prepared.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.
DetailsThis sample was mono disperse.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1394 / Average exposure time: 7.6 sec. / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56859
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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