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Yorodumi- EMDB-3777: Cryo EM structure of the bacterial disaggregase ClpB (BAP form, D... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3777 | |||||||||
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Title | Cryo EM structure of the bacterial disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state | |||||||||
Map data | ||||||||||
Sample |
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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 / protein refolding / response to heat / 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 / protein refolding / response to heat / response to oxidative stress / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Deville C / Carroni M / Franke KB / Topf M / Bukau B / Mogk A / Saibil HR | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3777.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-3777-v30.xml emd-3777.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3777_fsc.xml | 9 KB | Display | FSC data file |
Images | emd_3777.png | 37.4 KB | ||
Masks | emd_3777_msk_1.map | 64 MB | Mask map | |
Others | emd_3777_half_map_1.map.gz emd_3777_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3777 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3777 | HTTPS FTP |
-Validation report
Summary document | emd_3777_validation.pdf.gz | 537.3 KB | Display | EMDB validaton report |
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Full document | emd_3777_full_validation.pdf.gz | 536.4 KB | Display | |
Data in XML | emd_3777_validation.xml.gz | 15 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3777 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3777 | HTTPS FTP |
-Related structure data
Related structure data | 5og1MC 3776C 5ofoC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3777.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_3777_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_3777_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_3777_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ClpB homo hexamer, BAP form, double walker B mutant, in the ATPga...
Entire | Name: ClpB homo hexamer, BAP form, double walker B mutant, in the ATPgammaS state |
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Components |
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-Supramolecule #1: ClpB homo hexamer, BAP form, double walker B mutant, in the ATPga...
Supramolecule | Name: ClpB homo hexamer, BAP form, double walker B mutant, in the ATPgammaS state type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 570 KDa |
-Macromolecule #1: ClpB (BAP form, DWB mutant)
Macromolecule | Name: ClpB (BAP form, DWB mutant) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-5og1: |