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Yorodumi- EMDB-38537: Cryo-EM structure of ClpP1P2 in complex with ADEP1 from Streptomy... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38537 | |||||||||
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Title | Cryo-EM structure of ClpP1P2 in complex with ADEP1 from Streptomyces hawaiiensis | |||||||||
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Sample |
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Keywords | protease / protein degradation / proteostasis / proteolysis / HYDROLASE | |||||||||
Function / homology | Function and homology information endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Streptomyces hawaiiensis (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Xu X / Long F | |||||||||
Funding support | China, 1 items
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Citation | Journal: mBio / Year: 2024 Title: Structural insights into the Clp protein degradation machinery. Authors: Xiaolong Xu / Yanhui Wang / Wei Huang / Danyang Li / Zixin Deng / Feng Long / Abstract: The Clp protease system is important for maintaining proteostasis in bacteria. It consists of ClpP serine proteases and an AAA+ Clp-ATPase such as ClpC1. The hexameric ATPase ClpC1 utilizes the ...The Clp protease system is important for maintaining proteostasis in bacteria. It consists of ClpP serine proteases and an AAA+ Clp-ATPase such as ClpC1. The hexameric ATPase ClpC1 utilizes the energy of ATP binding and hydrolysis to engage, unfold, and translocate substrates into the proteolytic chamber of homo- or hetero-tetradecameric ClpP for degradation. The assembly between the hetero-tetradecameric ClpP1P2 chamber and the Clp-ATPases containing tandem ATPase domains from the same species has not been studied in depth. Here, we present cryo-EM structures of the substrate-bound ClpC1:shClpP1P2 from , and shClpP1P2 in complex with ADEP1, a natural compound produced by and known to cause over-activation and dysregulation of the ClpP proteolytic core chamber. Our structures provide detailed information on the shClpP1-shClpP2, shClpP2-ClpC1, and ADEP1-shClpP1/P2 interactions, reveal conformational transition of ClpC1 during the substrate translocation, and capture a rotational ATP hydrolysis mechanism likely dominated by the D1 ATPase activity of chaperones.IMPORTANCEThe Clp-dependent proteolysis plays an important role in bacterial homeostasis and pathogenesis. The ClpP protease system is an effective drug target for antibacterial therapy. can produce a class of potent acyldepsipeptide antibiotics such as ADEP1, which could affect the ClpP protease activity. Although hosts one of the most intricate ClpP systems in nature, very little was known about its Clp protease mechanism and the impact of ADEP molecules on ClpP. The significance of our research is in dissecting the functional mechanism of the assembled Clp degradation machinery, as well as the interaction between ADEP1 and the ClpP proteolytic chamber, by solving high-resolution structures of the substrate-bound Clp system in . The findings shed light on our understanding of the Clp-dependent proteolysis in bacteria, which will enhance the development of antimicrobial drugs targeting the Clp protease system, and help fighting against bacterial multidrug resistance. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38537.map.gz | 31.4 MB | EMDB map data format | |
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Header (meta data) | emd-38537-v30.xml emd-38537.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38537_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_38537.png | 271.5 KB | ||
Masks | emd_38537_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-38537.cif.gz | 5.9 KB | ||
Others | emd_38537_additional_1.map.gz emd_38537_half_map_1.map.gz emd_38537_half_map_2.map.gz | 57.2 MB 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38537 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38537 | HTTPS FTP |
-Validation report
Summary document | emd_38537_validation.pdf.gz | 851.9 KB | Display | EMDB validaton report |
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Full document | emd_38537_full_validation.pdf.gz | 851.4 KB | Display | |
Data in XML | emd_38537_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_38537_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38537 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38537 | HTTPS FTP |
-Related structure data
Related structure data | 8xopMC 8xn4C 8xonC 8xooC 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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-Map
File | Download / File: emd_38537.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: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_38537_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: sharpened
File | emd_38537_additional_1.map | ||||||||||||
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Annotation | sharpened | ||||||||||||
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-Half map: #2
File | emd_38537_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_38537_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : ClpP1,ClpP2
Entire | Name: ClpP1,ClpP2 |
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Components |
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-Supramolecule #1: ClpP1,ClpP2
Supramolecule | Name: ClpP1,ClpP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Streptomyces hawaiiensis (bacteria) |
-Macromolecule #1: ATP-dependent Clp protease proteolytic subunit
Macromolecule | Name: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp |
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Source (natural) | Organism: Streptomyces hawaiiensis (bacteria) |
Molecular weight | Theoretical: 22.632605 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MGLGDQVYNR LLNERIIFLG QPVDDDIANK ITAQLLLLAS DPEKDIYLYI NSPGGSITAG MAIYDTMQY IKNDVVTIAM GLAAAMGQFL LSAGTPGKRF ALPNAEILIH QPSAGLAGSA SDIKIHAERL LHTKKRMAEL T SQHTGQTI ...String: MGSSHHHHHH SSGLVPRGSH MGLGDQVYNR LLNERIIFLG QPVDDDIANK ITAQLLLLAS DPEKDIYLYI NSPGGSITAG MAIYDTMQY IKNDVVTIAM GLAAAMGQFL LSAGTPGKRF ALPNAEILIH QPSAGLAGSA SDIKIHAERL LHTKKRMAEL T SQHTGQTI EQITRDSDRD RWFDAFEAKE YGLIDDVMTT AAGMPGGGGT GA UniProtKB: ATP-dependent Clp protease proteolytic subunit |
-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: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp |
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Source (natural) | Organism: Streptomyces hawaiiensis (bacteria) |
Molecular weight | Theoretical: 24.05824 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSEYDPYA KLFEERVIFL GVQIDDASAN DVMAQLLCLE SMDPDRDISV YINSPGGSF TALTAIYDTM QYVKPDVQTV CMGQAAAAAA VLLAAGTPGK RMALPNARVL IHQPYSETGR GQVSDLEIAA N EILRMRSQ ...String: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSEYDPYA KLFEERVIFL GVQIDDASAN DVMAQLLCLE SMDPDRDISV YINSPGGSF TALTAIYDTM QYVKPDVQTV CMGQAAAAAA VLLAAGTPGK RMALPNARVL IHQPYSETGR GQVSDLEIAA N EILRMRSQ LEDMLAKHST TPVEKIREDI ERDKILTAED ALSYGLIDQV ISTRKMDNSS LR UniProtKB: ATP-dependent Clp protease proteolytic subunit |
-Macromolecule #3: ADEP1
Macromolecule | Name: ADEP1 / type: protein_or_peptide / ID: 3 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 736.855 Da |
Sequence | String: (OTT)FSP(MAA)A(MP8) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |