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Yorodumi- EMDB-20422: ClpX in ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20422 | |||||||||
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Title | ClpX in ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 1 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information protein denaturation / HslUV protease complex / endopeptidase Clp complex / ATP-dependent peptidase activity / protein unfolding / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protein folding ...protein denaturation / HslUV protease complex / endopeptidase Clp complex / ATP-dependent peptidase activity / protein unfolding / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protein folding / peptidase activity / protease binding / protein dimerization activity / cell division / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.12 Å | |||||||||
Authors | Fei X / Jenni S / Harrison SC / Sauer RT | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Elife / Year: 2020 Title: Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate. Authors: Xue Fei / Tristan A Bell / Simon Jenni / Benjamin M Stinson / Tania A Baker / Stephen C Harrison / Robert T Sauer / Abstract: ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the ...ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results. | |||||||||
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_20422.map.gz | 21.3 MB | EMDB map data format | |
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Header (meta data) | emd-20422-v30.xml emd-20422.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20422_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_20422.png | 88.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20422 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20422 | HTTPS FTP |
-Validation report
Summary document | emd_20422_validation.pdf.gz | 370.6 KB | Display | EMDB validaton report |
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Full document | emd_20422_full_validation.pdf.gz | 370.2 KB | Display | |
Data in XML | emd_20422_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | emd_20422_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20422 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20422 | HTTPS FTP |
-Related structure data
Related structure data | 6pp8MC 6po1C 6po3C 6podC 6posC 6pp5C 6pp6C 6pp7C 6ppeC 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_20422.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ClpX-ClpP-substrate-ATPrS
Entire | Name: ClpX-ClpP-substrate-ATPrS |
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Components |
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-Supramolecule #1: ClpX-ClpP-substrate-ATPrS
Supramolecule | Name: ClpX-ClpP-substrate-ATPrS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: ER2566 |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: ER2566 |
-Macromolecule #1: ATP-dependent Clp protease ATP-binding subunit ClpX
Macromolecule | Name: ATP-dependent Clp protease ATP-binding subunit ClpX / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 39.835129 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SALPTPHEIR NHLDDYVIGQ EQAKKVLAVA VYNHYKRLRN GDTSNGVELG KSNILLIGPT GSGKTLLAET LARLLDVPFT MADATTLTE AGYVGEDVEN IIQKLLQKSD YDVQKAQRGI VYIDQIDKIS RKSDNPSITR DVSGEGVQQA LLKLIEGTVA A VPPQGGRK ...String: SALPTPHEIR NHLDDYVIGQ EQAKKVLAVA VYNHYKRLRN GDTSNGVELG KSNILLIGPT GSGKTLLAET LARLLDVPFT MADATTLTE AGYVGEDVEN IIQKLLQKSD YDVQKAQRGI VYIDQIDKIS RKSDNPSITR DVSGEGVQQA LLKLIEGTVA A VPPQGGRK HPQQEFLQVD TSKILFICGG AFAGLDKVIS HRVETGSGIG FGATVKAKSD KASEGELLAQ VEPEDLIKFG LI PEFIGRL PVVATLNELS EEALIQILKE PKNALTKQYQ ALFNLEGVDL EFRDEALDAI AKKAMARKTG ARGLRSIVEA ALL DTMYDL PSMEDVEKVV IDESVIDGQS EPLLIYGKPE AQQASGEGGG TSG |
-Macromolecule #2: substrate peptide
Macromolecule | Name: substrate peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 770.943 Da |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)R(UNK)(UNK)(UNK) |
-Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 5 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Average exposure time: 60.0 sec. / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: -2.5 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus min: -0.8 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |