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- PDB-5vy9: S. cerevisiae Hsp104:casein complex, Middle Domain Conformation -

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Basic information

Entry
Database: PDB / ID: 5vy9
TitleS. cerevisiae Hsp104:casein complex, Middle Domain Conformation
Components
  • Alpha-S1-casein
  • Heat shock protein 104
KeywordsCHAPERONE / Hsp104 / cryoem / AAA+
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Heat shock protein 104
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Bos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsGates, S.N. / Yokom, A.L. / Lin, J.-B. / Jackrel, M.E. / Rizo, A.N. / Kendsersky, N.M. / Buell, C.E. / Sweeny, E.A. / Chuang, E. / Torrente, M.P. ...Gates, S.N. / Yokom, A.L. / Lin, J.-B. / Jackrel, M.E. / Rizo, A.N. / Kendsersky, N.M. / Buell, C.E. / Sweeny, E.A. / Chuang, E. / Torrente, M.P. / Mack, K.L. / Su, M. / Shorter, J. / Southworth, D.R.
CitationJournal: Science / Year: 2017
Title: Ratchet-like polypeptide translocation mechanism of the AAA+ disaggregase Hsp104.
Authors: Stephanie N Gates / Adam L Yokom / JiaBei Lin / Meredith E Jackrel / Alexandrea N Rizo / Nathan M Kendsersky / Courtney E Buell / Elizabeth A Sweeny / Korrie L Mack / Edward Chuang / Mariana ...Authors: Stephanie N Gates / Adam L Yokom / JiaBei Lin / Meredith E Jackrel / Alexandrea N Rizo / Nathan M Kendsersky / Courtney E Buell / Elizabeth A Sweeny / Korrie L Mack / Edward Chuang / Mariana P Torrente / Min Su / James Shorter / Daniel R Southworth /
Abstract: Hsp100 polypeptide translocases are conserved members of the AAA+ family (adenosine triphosphatases associated with diverse cellular activities) that maintain proteostasis by unfolding aberrant and ...Hsp100 polypeptide translocases are conserved members of the AAA+ family (adenosine triphosphatases associated with diverse cellular activities) that maintain proteostasis by unfolding aberrant and toxic proteins for refolding or proteolytic degradation. The Hsp104 disaggregase from solubilizes stress-induced amorphous aggregates and amyloids. The structural basis for substrate recognition and translocation is unknown. Using a model substrate (casein), we report cryo-electron microscopy structures at near-atomic resolution of Hsp104 in different translocation states. Substrate interactions are mediated by conserved, pore-loop tyrosines that contact an 80-angstrom-long unfolded polypeptide along the axial channel. Two protomers undergo a ratchet-like conformational change that advances pore loop-substrate interactions by two amino acids. These changes are coupled to activation of specific nucleotide hydrolysis sites and, when transmitted around the hexamer, reveal a processive rotary translocation mechanism and substrate-responsive flexibility during Hsp104-catalyzed disaggregation.
History
DepositionMay 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 15, 2018Group: Data collection / Data processing / Category: em_3d_reconstruction / Item: _em_3d_reconstruction.resolution
Revision 1.3Nov 20, 2019Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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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
P: Alpha-S1-casein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)621,72419
Polymers615,4457
Non-polymers6,27912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area59960 Å2
ΔGint-150 kcal/mol
Surface area202660 Å2

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Components

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


Mass: 102173.961 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HSP104, YLL026W, L0948 / Production host: Escherichia coli (E. coli) / References: UniProt: P31539
#2: Protein/peptide Alpha-S1-casein


Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: protein was purchased from Sigma-Aldrich. purified from bovine milk
Source: (natural) Bos taurus (cattle)
#3: 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.: 12 / Source method: obtained synthetically / 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 / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1S. cerevisiae Hsp104:casein complex, Middle Domain ConformationCOMPLEX#1-#20MULTIPLE SOURCES
2Hsp104COMPLEX#11RECOMBINANT
3caseinCOMPLEX#21NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292ATCC 204508 / S288c
33Bos taurus (cattle)9913
Source (recombinant)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 0.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Image processingDetails: Removed first 2 frames from movie before drift correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146463 / Symmetry type: POINT

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