[English] 日本語
Yorodumi
- EMDB-3777: Cryo EM structure of the bacterial disaggregase ClpB (BAP form, D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3777
TitleCryo EM structure of the bacterial disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state
Map data
Sample
  • Complex: ClpB homo hexamer, BAP form, double walker B mutant, in the ATPgammaS state
    • Protein or peptide: ClpB (BAP form, DWB mutant)
Function / homology
Function and homology information


endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / cellular response to heat / response to heat / protein refolding / response to oxidative stress / ATP hydrolysis activity / ATP binding ...endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / cellular response to heat / response to heat / protein refolding / response to oxidative stress / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
ATP-dependent Clp protease ATP-binding subunit ClpA / Chaperonin ClpB / 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 profile. ...ATP-dependent Clp protease ATP-binding subunit ClpA / Chaperonin ClpB / 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 profile. / Clp, repeat (R) domain / 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
ATP-dependent Clp protease ATP-binding subunit ClpA / Chaperone protein ClpB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsDeville C / Carroni M / Franke KB / Topf M / Bukau B / Mogk A / Saibil HR
CitationJournal: Sci Adv / Year: 2017
Title: Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase.
Authors: Célia Deville / Marta Carroni / Kamila B Franke / Maya Topf / Bernd Bukau / Axel Mogk / Helen R Saibil /
Abstract: Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including ClpB, form a powerful disaggregation machine that threads ...Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo-electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5'--(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam. In the substrate-free state, a marked gradient of resolution, likely corresponding to mobility, spans across the AAA+ rings with a dynamic hotspot at the seam. On the seam side, the coiled-coil regulatory domains are locked in a horizontal, inactive orientation. On the opposite side, the regulatory domains are accessible for Hsp70 binding, substrate targeting, and activation. In the presence of the model substrate casein, the polypeptide threads through the entire pore channel and increased nucleotide occupancy correlates with higher ATPase activity. Substrate-induced domain displacements indicate a pathway of regulated substrate transfer from Hsp70 to the ClpB pore, inside which a spiral of loops contacts the substrate. The seam pore loops undergo marked displacements, along with ordering of the regulatory domains. These asymmetric movements suggest a mechanism for ATPase activation and substrate threading during disaggregation.
History
DepositionJun 22, 2017-
Header (metadata) releaseAug 16, 2017-
Map releaseAug 16, 2017-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5og1
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3777.png

Downloads & links

-
Map

FileDownload / File: emd_3777.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1
Minimum - Maximum-1.5949053 - 3.7573104
Average (Standard dev.)0.011806805 (±0.22490339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 355.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z355.840355.840355.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.5953.7570.012

-
Supplemental data

-
Mask #1

Fileemd_3777_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_3777_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_3777_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ClpB homo hexamer, BAP form, double walker B mutant, in the ATPga...

EntireName: ClpB homo hexamer, BAP form, double walker B mutant, in the ATPgammaS state
Components
  • Complex: ClpB homo hexamer, BAP form, double walker B mutant, in the ATPgammaS state
    • Protein or peptide: ClpB (BAP form, DWB mutant)

-
Supramolecule #1: ClpB homo hexamer, BAP form, double walker B mutant, in the ATPga...

SupramoleculeName: ClpB homo hexamer, BAP form, double walker B mutant, in the ATPgammaS state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 570 KDa

-
Macromolecule #1: ClpB (BAP form, DWB mutant)

MacromoleculeName: ClpB (BAP form, DWB mutant) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLDRLTNKF QLALADAQSL ALGHDNQFIE PLHLMSALLN QEGGSVSPLL TSAGINAGQL RTDINQALNR LPQVEGTGGD VQPSQDLVRV LNLCDKLAQK RGDNFISSEL FVLAALESRG TLADILKAAG ATTANITQAI EQMRGGESVN DQGAEDQRQA LKKYTIDLTE ...String:
MRLDRLTNKF QLALADAQSL ALGHDNQFIE PLHLMSALLN QEGGSVSPLL TSAGINAGQL RTDINQALNR LPQVEGTGGD VQPSQDLVRV LNLCDKLAQK RGDNFISSEL FVLAALESRG TLADILKAAG ATTANITQAI EQMRGGESVN DQGAEDQRQA LKKYTIDLTE RAEQGKLDPV IGRDEEIRRT IQVLQRRTKN NPVLIGEPGV GKTAIVEGLA QRIINGEVPE GLKGRRVLAL DMGALVAGAK YRGEFEERLK GVLNDLAKQE GNVILFIDQL HTMVGAGKAD GAMDAGNMLK PALARGELHC VGATTLDEYR QYIEKDAALE RRFQKVFVAE PSVEDTIAIL RGLKERYELH HHVQITDPAI VAAATLSHRY IADRQLPDKA IDLIDEAASS IRMQIDSKPE ELDRLDRRII QLKLEQQALM KESDEASKKR LDMLNEELSD KERQYSELEE EWKAEKASLS GTQTIKAELE QAKIAIEQAR RVGDLARMSE LQYGKIPELE KQLEAATQLE GKTMRLLRNK VTDAEIAEVL ARWTGIPVSR MMESEREKLL RMEQELHHRV IGQNEAVDAV SNAIRRSRAG LADPNRPIGS FLFLGPTGVG KTELCKALAN FMFDSDEAMV RIDMSEFMEK HSVSRLVGAP PGYVGYEEGG YLTEAVRRRP YSVILLDQVE KAHPDVFNIL LQVLDDGRLT DGQGRTVDFR NTVVIMTSNL GVRETERKSI GLIHQDNSTD AMEEIKKIFR PEFINRIDEV VVFHPLGEQH IASIAQIQLK RLYKRLEERG YEIHISDEAL KLLSENGYDP VYGARPLKRA IQQQIENPLA QQILSGELVP GKVIRLEVNE DRIVAVQH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mol/LTrisHClTrisHCl
25.0 mol/LNaClSodium chloridesodium chloride
10.0 mol/LMgCl2magnesium chloride
2.0 mol/LATPgSadenosine 5'-O-(3-thio)triphosphate
1.0 mol/LDTTdithiothreitol
GridMaterial: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 100000
Specialist opticsEnergy filter - Name: GIF
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER / Details: filtered map from EMD-3776
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60000
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5og1:
Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state

+
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