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- EMDB-8745: S. cerevisiae Hsp104:casein complex, Middle Domain Conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-8745
TitleS. cerevisiae Hsp104:casein complex, Middle Domain Conformation
Map dataHsp104:casein complex, Middle Domain Conformation
Sample
  • Complex: S. cerevisiae Hsp104:casein complex, Middle Domain Conformation
    • Complex: Hsp104
      • Protein or peptide: Heat shock protein 104
    • Complex: casein
      • Protein or peptide: Alpha-S1-casein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsHsp104 / cryoem / AAA+ / 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 (strain ATCC 204508 / S288c) (yeast) / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsGates SN / Yokom AL
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, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseJul 19, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0222
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0222
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5vy9
  • Surface level: 0.0222
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8745.png

Downloads & links

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Map

FileDownload / File: emd_8745.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHsp104:casein complex, Middle Domain Conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0222 / Movie #1: 0.0222
Minimum - Maximum-0.040255334 - 0.08343841
Average (Standard dev.)0.000802514 (±0.0043818736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0400.0830.001

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Supplemental data

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Sample components

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Entire : S. cerevisiae Hsp104:casein complex, Middle Domain Conformation

EntireName: S. cerevisiae Hsp104:casein complex, Middle Domain Conformation
Components
  • Complex: S. cerevisiae Hsp104:casein complex, Middle Domain Conformation
    • Complex: Hsp104
      • Protein or peptide: Heat shock protein 104
    • Complex: casein
      • Protein or peptide: Alpha-S1-casein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: S. cerevisiae Hsp104:casein complex, Middle Domain Conformation

SupramoleculeName: S. cerevisiae Hsp104:casein complex, Middle Domain Conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Supramolecule #2: Hsp104

SupramoleculeName: Hsp104 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: casein

SupramoleculeName: casein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bos taurus (cattle)

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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: 102.173961 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 IVIMTSNLGA 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: Alpha-S1-casein

MacromoleculeName: Alpha-S1-casein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 2.400951 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 12 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsRemoved first 2 frames from movie before drift correction
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146463
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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