+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27952 | |||||||||
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Title | Cryo-EM structure of substrate-free ClpX.ClpP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | AAA+ protease / ClpXP / substrate-free / CHAPERONE | |||||||||
Function / homology | Function and homology information HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteasomal protein catabolic process / serine-type peptidase activity / proteolysis involved in protein catabolic process ...HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteasomal protein catabolic process / serine-type peptidase activity / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / ATPase binding / peptidase activity / response to heat / protein dimerization activity / cell division / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.57 Å | |||||||||
Authors | Ghanbarpour A / Davis JH / Sauer RT | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of substrate-free DNClpX.ClpP Authors: Ghanbarpour A / Cohen S / Davis JH / Sauer RT | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27952.map.gz | 32.5 MB | EMDB map data format | |
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Header (meta data) | emd-27952-v30.xml emd-27952.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27952_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_27952.png | 52 KB | ||
Masks | emd_27952_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-27952.cif.gz | 5.8 KB | ||
Others | emd_27952_half_map_1.map.gz emd_27952_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27952 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27952 | HTTPS FTP |
-Validation report
Summary document | emd_27952_validation.pdf.gz | 993.4 KB | Display | EMDB validaton report |
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Full document | emd_27952_full_validation.pdf.gz | 993 KB | Display | |
Data in XML | emd_27952_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_27952_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27952 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27952 | HTTPS FTP |
-Related structure data
Related structure data | 8e91MC 8e7vC 8e8qC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27952.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: 1.124 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27952_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27952_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27952_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ClpXP AAA protease
Entire | Name: ClpXP AAA protease |
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Components |
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-Supramolecule #1: ClpXP AAA protease
Supramolecule | Name: ClpXP AAA protease / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-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: 46.414848 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTDKRKDGSG KLLYCSFCGK SQHEVRKLIA GPSVYICDEC VDLCNDIIRE EIKEVAPHRE RSALPTPHEI RNHLDDYVIG QEQAKKVLA VAVYNHYKRL RNGDTSNGVE LGKSNILLIG PTGSGKTLLA ETLARLLDVP FTMADATTLT EAGYVGEDVE N IIQKLLQK ...String: MTDKRKDGSG KLLYCSFCGK SQHEVRKLIA GPSVYICDEC VDLCNDIIRE EIKEVAPHRE RSALPTPHEI RNHLDDYVIG QEQAKKVLA VAVYNHYKRL RNGDTSNGVE LGKSNILLIG PTGSGKTLLA ETLARLLDVP FTMADATTLT EAGYVGEDVE N IIQKLLQK CDYDVQKAQR GIVYIDEIDK ISRKSDNPSI TRDVSGEGVQ QALLKLIEGT VAAVPPQGGR KHPQQEFLQV DT SKILFIC GGAFAGLDKV ISHRVETGSG IGFGATVKAK SDKASEGELL AQVEPEDLIK FGLIPEFIGR LPVVATLNEL SEE ALIQIL KEPKNALTKQ YQALFNLEGV DLEFRDEALD AIAKKAMARK TGARGLRSIV EAALLDTMYD LPSMEDVEKV VIDE SVIDG QSEPLLIYGK PEAQQASGE UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpX |
-Macromolecule #2: ATP-dependent Clp protease proteolytic subunit
Macromolecule | Name: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO / EC number: endopeptidase Clp |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 23.468869 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: LVPMVIEQTS RGERSFDIYS RLLKERVIFL TGQVEDHMAN LIVAQMLFLE AENPEKDIYL YINSPGGVIT AGMSIYDTMQ FIKPDVSTI CMGQAASMGA FLLTAGAKGK RFCLPNSRVM IHQPLGGYQG QATDIEIHAR EILKVKGRMN ELMALHTGQS L EQIERDTE ...String: LVPMVIEQTS RGERSFDIYS RLLKERVIFL TGQVEDHMAN LIVAQMLFLE AENPEKDIYL YINSPGGVIT AGMSIYDTMQ FIKPDVSTI CMGQAASMGA FLLTAGAKGK RFCLPNSRVM IHQPLGGYQG QATDIEIHAR EILKVKGRMN ELMALHTGQS L EQIERDTE RDRFLSAPEA VEYGLVDSIL THRNENLYFQ SLEHHHHHH UniProtKB: ATP-dependent Clp protease proteolytic subunit |
-Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 4 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / 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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.67 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: 1.75 µm / Nominal defocus min: 0.3 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |