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Yorodumi- EMDB-15241: Mycobacterium tuberculosis ClpC1 hexamer structure bound to the n... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15241 | ||||||||||||
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Title | Mycobacterium tuberculosis ClpC1 hexamer structure bound to the natural product antibiotic Cyclomarin | ||||||||||||
Map data | Sharpened map of Mycobacterium tuberculosis ClpC1 cyclomarin | ||||||||||||
Sample |
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Function / homology | Function and homology information protein folding chaperone / peptidoglycan-based cell wall / cellular response to heat / protein homodimerization activity / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.34 Å | ||||||||||||
Authors | Felix J / Fraga H / Gragera M / Bueno T / Weinhaeupl K | ||||||||||||
Funding support | European Union, 3 items
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Citation | Journal: J Biol Chem / Year: 2022 Title: Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action. Authors: Katharina Weinhäupl / Marcos Gragera / M Teresa Bueno-Carrasco / Rocío Arranz / Olga Krandor / Tatos Akopian / Raquel Soares / Eric Rubin / Jan Felix / Hugo Fraga / Abstract: The unfoldase ClpC1 is one of the most exciting drug targets against tuberculosis. This AAA+ unfoldase works in cooperation with the ClpP1P2 protease and is the target of at least four natural ...The unfoldase ClpC1 is one of the most exciting drug targets against tuberculosis. This AAA+ unfoldase works in cooperation with the ClpP1P2 protease and is the target of at least four natural product antibiotics: cyclomarin, ecumicin, lassomycin, and rufomycin. Although these molecules are promising starting points for drug development, their mechanisms of action remain largely unknown. Taking advantage of a middle domain mutant, we determined the first structure of Mycobacterium tuberculosis ClpC1 in its apo, cyclomarin-, and ecumicin-bound states via cryo-EM. The obtained structure displays features observed in other members of the AAA+ family and provides a map for further drug development. While the apo and cyclomarin-bound structures are indistinguishable and have N-terminal domains that are invisible in their respective EM maps, around half of the ecumicin-bound ClpC1 particles display three of their six N-terminal domains in an extended conformation. Our structural observations suggest a mechanism where ecumicin functions by mimicking substrate binding, leading to ATPase activation and changes in protein degradation profile. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15241.map.gz | 450.2 MB | EMDB map data format | |
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Header (meta data) | emd-15241-v30.xml emd-15241.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15241_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_15241.png | 101.1 KB | ||
Masks | emd_15241_msk_1.map | 476.8 MB | Mask map | |
Others | emd_15241_additional_1.map.gz emd_15241_half_map_1.map.gz emd_15241_half_map_2.map.gz | 421.7 MB 442.4 MB 442.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15241 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15241 | HTTPS FTP |
-Validation report
Summary document | emd_15241_validation.pdf.gz | 853.5 KB | Display | EMDB validaton report |
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Full document | emd_15241_full_validation.pdf.gz | 853.1 KB | Display | |
Data in XML | emd_15241_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | emd_15241_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15241 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15241 | HTTPS FTP |
-Related structure data
Related structure data | 8a8vMC 8a8uC 8a8wC C: citing same article (ref.) M: atomic model generated by this map |
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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_15241.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map of Mycobacterium tuberculosis ClpC1 cyclomarin | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.855 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15241_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: DeepEMhancer sharpened map of Mycobacterium tuberculosis ClpC1 cyclomarin...
File | emd_15241_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer sharpened map of Mycobacterium tuberculosis ClpC1 cyclomarin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15241_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15241_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mycobacterium tuberculosis ClpC1 in complex with the natural prod...
Entire | Name: Mycobacterium tuberculosis ClpC1 in complex with the natural product antibiotic Cyclomarin |
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Components |
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-Supramolecule #1: Mycobacterium tuberculosis ClpC1 in complex with the natural prod...
Supramolecule | Name: Mycobacterium tuberculosis ClpC1 in complex with the natural product antibiotic Cyclomarin type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 567 KDa |
-Macromolecule #1: ATP-dependent Clp protease ATP-binding subunit ClpC1
Macromolecule | Name: ATP-dependent Clp protease ATP-binding subunit ClpC1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases) |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv |
Molecular weight | Theoretical: 94.758695 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MFERFTDRAR RVVVLAQEEA RMLNHNYIGT EHILLGLIHE GEGVAAKSLE SLGISLEGVR SQVEEIIGQG QQAPSGHIPF TPRAKKVLE LSLREALQLG HNYIGTEHIL LGLIREGEGV AAQVLVKLGA ELTRVRQQVI QLLSGYQGKE AAEAGTGGRG G ESGSPSTS ...String: MFERFTDRAR RVVVLAQEEA RMLNHNYIGT EHILLGLIHE GEGVAAKSLE SLGISLEGVR SQVEEIIGQG QQAPSGHIPF TPRAKKVLE LSLREALQLG HNYIGTEHIL LGLIREGEGV AAQVLVKLGA ELTRVRQQVI QLLSGYQGKE AAEAGTGGRG G ESGSPSTS LVLDQFGRNL TAAAMEGKLD PVIGREKEIE RVMQVLSRRT KNNPVLIGEP GVGKTAVVEG LAQAIVHGEV PE TLKDKQL YTLDLGSLVA GSRYRGDFEE RLKKVLKEIN TRGDIILFID ELHTLVGAGA AEGAIDAASI LKPKLARGEL QTI GATTLD EYRKYIEKDA ALERRFQPVQ VGEPTVEHTI EILKGLRDRY EAHHRVSITD AAMVAAATLA DRYINDRFLP DKAI DLIDE AGARMRIRRM TAPPDLREFD EKIAEARREK ESAIDAQDFE KAASLRDREK TLVAQRAERE KQWRSGDLDV VAEVD DEQI AEVLGNWTGI PVFKLTEAET TRLLRMEEEL HKRIIGQEDA VKAVSKAIRR TRAGLKDPKR PSGSFIFAGP SGVGKT ELS KALANFLFGD DDALIQIDMG EFHDRFTASR LFGAPPGYVG YEEGGQLTEK VRRKPFSVVL FDEIEKAHQE IYNSLLQ VL EDGRLTDGQG RTVDFKNTVL IFTSNLGTSD ISKPVGLGFS KGGGENDYER MKQKVNDELK KHFRPEFLNR IDDIIVFH Q LTREEIIRMV DLMISRVAGQ LKSKDMALVL TDAAKALLAK RGFDPVLGAR PLRRTIQREI EDQLSEKILF EEVGPGQVV TVDVDNWDGE GPGEDAVFTF TGTRKPPAEP DLAKAGAHSA GGPEPAARLE HHHHHH |
-Macromolecule #2: Bound polypeptide
Macromolecule | Name: Bound polypeptide / type: protein_or_peptide / ID: 2 / Details: The actual sequence of the polypeptide is unknown. / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Molecular weight | Theoretical: 1.975426 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 10 / 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
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 Details: Hepes pH 7.4 50 mM, NaCl 100 mM, 10 mM MgCl2, ATP 1mM |
Vitrification | Cryogen name: ETHANE |
Details | 10 microM ClpC1 with 30 microM Cyclomarin |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 30.0 sec. / Average electron dose: 36.9 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |