[English] 日本語
Yorodumi
- EMDB-8697: Closed State CryoEM Reconstruction of Hsp104:ATPyS and FITC casein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8697
TitleClosed State CryoEM Reconstruction of Hsp104:ATPyS and FITC casein
Map dataClosed State of Hsp104:ATPyS and FITC casein
Sample
  • Complex: Hsp104 ATPyS and FITC casein in Closed State
    • Protein or peptide: Heat shock protein 104
    • Protein or peptide: FITC casein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsHsp104 / cryoem / AAA+ / CHAPERONE
Function / homology
Function and homology information


: / TRC complex / protein folding in endoplasmic reticulum / cellular heat acclimation / post-translational protein targeting to endoplasmic reticulum membrane / stress granule disassembly / : / protein unfolding / nuclear periphery / ADP binding ...: / TRC complex / protein folding in endoplasmic reticulum / cellular heat acclimation / post-translational protein targeting to endoplasmic reticulum membrane / stress granule disassembly / : / 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) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsGates SN
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
DepositionApr 19, 2017-
Header (metadata) releaseJul 5, 2017-
Map releaseJul 5, 2017-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0283
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0283
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5vjh
  • Surface level: 0.0283
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8697.png

Downloads & links

-
Map

FileDownload / File: emd_8697.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClosed State of Hsp104:ATPyS and FITC casein
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: 0.0283 / Movie #1: 0.0283
Minimum - Maximum-0.08479348 - 0.16786447
Average (Standard dev.)0.0006029298 (±0.0056465184)
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-0.0850.1680.001

-
Supplemental data

-
Sample components

-
Entire : Hsp104 ATPyS and FITC casein in Closed State

EntireName: Hsp104 ATPyS and FITC casein in Closed State
Components
  • Complex: Hsp104 ATPyS and FITC casein in Closed State
    • Protein or peptide: Heat shock protein 104
    • Protein or peptide: FITC casein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

-
Supramolecule #1: Hsp104 ATPyS and FITC casein in Closed State

SupramoleculeName: Hsp104 ATPyS and FITC casein in Closed State / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
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 K-12 (bacteria)
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

-
Macromolecule #2: FITC casein

MacromoleculeName: FITC casein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 2.230741 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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
Image processing

DetailsRemoved first 2 frames from movie before drift correction
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146463
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more