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Yorodumi- EMDB-27941: Cryo-EM structure of substrate-free DNClpX.ClpP from singly cappe... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27941 | |||||||||
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Title | Cryo-EM structure of substrate-free DNClpX.ClpP from singly capped particles | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ClpXP / AAA protease / substrate-free cryo-EM / CHAPERONE | |||||||||
Function / homology | Function and homology information protein denaturation / 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 / protein unfolding / proteasomal protein catabolic process ...protein denaturation / 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 / protein unfolding / proteasomal protein catabolic process / serine-type peptidase activity / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / response to radiation / disordered domain specific binding / unfolded protein binding / ATPase binding / response to heat / protease binding / 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: 3.1 Å | |||||||||
Authors | Ghanbarpour A / Cohen S / 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_27941.map.gz | 52.2 MB | EMDB map data format | |
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Header (meta data) | emd-27941-v30.xml emd-27941.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27941_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_27941.png | 74.1 KB | ||
Masks | emd_27941_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-27941.cif.gz | 5.9 KB | ||
Others | emd_27941_half_map_1.map.gz emd_27941_half_map_2.map.gz | 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27941 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27941 | HTTPS FTP |
-Related structure data
Related structure data | 8e7vMC 8e8qC 8e91C 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_27941.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.249 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27941_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27941_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27941_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: 42.355812 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH DYDIPTTENL YFQGSSALPT PHEIRNHLDD YVIGQEQAKK VLAVAVYNHY KRLRNGDTSN GVELGKSNIL LIGPTGSGK TLLAETLARL LDVPFTMADA TTLTEAGYVG EDVENIIQKL LQKSDYDVQK AQRGIVYIDE IDKISRKSDN P SITRDVSG ...String: MGSSHHHHHH DYDIPTTENL YFQGSSALPT PHEIRNHLDD YVIGQEQAKK VLAVAVYNHY KRLRNGDTSN GVELGKSNIL LIGPTGSGK TLLAETLARL LDVPFTMADA TTLTEAGYVG EDVENIIQKL LQKSDYDVQK AQRGIVYIDE IDKISRKSDN P SITRDVSG EGVQQALLKL IEGTVAAVPP QGGRKHPQQE FLQVDTSKIL FICGGAFAGL DKVISHRVET GSGIGFGATV KA KSDKASE GELLAQVEPE DLIKFGLIPE FIGRLPVVAT LNELSEEALI QILKEPKNAL TKQYQALFNL EGVDLEFRDE ALD AIAKKA MARKTGARGL RSIVEAALLD TMYDLPSMED VEKVVIDESV IDGQSEPLLI YGKPEAQQAS GE 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: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-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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Grid | Model: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-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: 49.39 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |