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Yorodumi- EMDB-34136: Complex structure of Clostridioides difficile binary toxin folded... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34136 | |||||||||
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Title | Complex structure of Clostridioides difficile binary toxin folded CDTa-bound CDTb-pore (short). | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / Translocation / Oligomer / Unfoldase / TOXIN | |||||||||
Function / homology | Function and homology information protein homooligomerization / transferase activity / nucleotide binding / extracellular region / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridioides difficile (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.18 Å | |||||||||
Authors | Yamada T / Kawamoto A / Yoshida T / Sato Y / Kato T / Tsuge H | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile. Authors: Akihiro Kawamoto / Tomohito Yamada / Toru Yoshida / Yusui Sato / Takayuki Kato / Hideaki Tsuge / Abstract: Some bacteria express a binary toxin translocation system, consisting of an enzymatic subunit and translocation pore, that delivers enzymes into host cells through endocytosis. The most clinically ...Some bacteria express a binary toxin translocation system, consisting of an enzymatic subunit and translocation pore, that delivers enzymes into host cells through endocytosis. The most clinically important bacterium with such a system is Clostridioides difficile (formerly Clostridium). The CDTa and CDTb proteins from its system represent important therapeutic targets. CDTb has been proposed to be a di-heptamer, but its physiological heptameric structure has not yet been reported. Here, we report the cryo-EM structure of CDTa bound to the CDTb-pore, which reveals that CDTa binding induces partial unfolding and tilting of the first CDTa α-helix. In the CDTb-pore, an NSS-loop exists in 'in' and 'out' conformations, suggesting its involvement in substrate translocation. Finally, 3D variability analysis revealed CDTa movements from a folded to an unfolded state. These dynamic structural information provide insights into drug design against hypervirulent C. difficile strains. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34136.map.gz | 290.7 MB | EMDB map data format | |
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Header (meta data) | emd-34136-v30.xml emd-34136.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
Images | emd_34136.png | 100.3 KB | ||
Filedesc metadata | emd-34136.cif.gz | 6.3 KB | ||
Others | emd_34136_additional_1.map.gz emd_34136_half_map_1.map.gz emd_34136_half_map_2.map.gz | 153.9 MB 285.6 MB 285.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34136 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34136 | HTTPS FTP |
-Validation report
Summary document | emd_34136_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_34136_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_34136_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_34136_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34136 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34136 | HTTPS FTP |
-Related structure data
Related structure data | 7yvqMC 7vnjC 7vnnC 7yvsC 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_34136.map.gz / Format: CCP4 / Size: 307.5 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: 0.88 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_34136_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_34136_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34136_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Clostridioides difficile transferase complex
Entire | Name: Clostridioides difficile transferase complex |
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Components |
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-Supramolecule #1: Clostridioides difficile transferase complex
Supramolecule | Name: Clostridioides difficile transferase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Clostridioides difficile (bacteria) |
-Macromolecule #1: ADP-ribosylating binary toxin binding subunit CdtB
Macromolecule | Name: ADP-ribosylating binary toxin binding subunit CdtB / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridioides difficile (bacteria) |
Molecular weight | Theoretical: 75.657141 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: NNNFFDPKLM SDWEDEDLDT DNDNIPDSYE RNGYTIKDLI AVKWEDSFAE QGYKKYVSNY LESNTAGDPY TDYEKASGSF DKAIKTEAR DPLVAAYPIV GVGMEKLIIS TNEHASTDQG KTVSRATTNS KTESNTAGVS VNVGYQNGFT ANVTTNYSHT T DNSTAVQD ...String: NNNFFDPKLM SDWEDEDLDT DNDNIPDSYE RNGYTIKDLI AVKWEDSFAE QGYKKYVSNY LESNTAGDPY TDYEKASGSF DKAIKTEAR DPLVAAYPIV GVGMEKLIIS TNEHASTDQG KTVSRATTNS KTESNTAGVS VNVGYQNGFT ANVTTNYSHT T DNSTAVQD SNGESWNTGL SINKGESAYI NANVRYYNTG TAPMYKVTPT TNLVLDGDTL STIKAQENQI GNNLSPGDTY PK KGLSPLA LNTMDQFSSR LIPINYDQLK KLDAGKQIKL ETTQVSGNFG TKNSSGQIVT EGNSWSDYIS QIDSISASII LDT ENESYE RRVTAKNLQD PEDKTPELTI GEAIEKAFGA TKKDGLLYFN DIPIDESCVE LIFDDNTANK IKDSLKTLSD KKIY NVKLE RGMNILIKTP TYFTNFDDYN NYPSTWSNVN TTNQDGLQGS ANKLNGETKI KIPMSELKPY KRYVFSGYSK DPLTS NSII VKIKAKEEKT DYLVPEQGYT KFSYEFETTE KDSSNIEITL IGSGTTYLDN LSITELNSTP EILDEPEVKI PTDQEI MDA HKIYFADLNF NPSTGNTYIN GMYFAPTQTN KEALDYIQKY RVEATLQYSG FKDIGTKDKE MRNYLGDPNQ PKTNYVN LR SYFTGGENIM TYKKLRIYAI TPDDRELLVL SVD UniProtKB: ADP-ribosyltransferase binding component |
-Macromolecule #2: ADP-ribosylating binary toxin enzymatic subunit CdtA
Macromolecule | Name: ADP-ribosylating binary toxin enzymatic subunit CdtA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridioides difficile (bacteria) |
Molecular weight | Theoretical: 49.420469 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: APIERPEDFL KDKEKAKEWE RKEAERIEQK LERSEKEALE SYKKDSVEIS KYSQTRNYFY DYQIEANSRE KEYKELRNAI SKNKIDKPM YVYYFESPEK FAFNKVIRTE NQNEISLEKF NEFKETIQNK LFKQDGFKDI SLYEPGKGDE KPTPLLMHLK L PRNTGMLP ...String: APIERPEDFL KDKEKAKEWE RKEAERIEQK LERSEKEALE SYKKDSVEIS KYSQTRNYFY DYQIEANSRE KEYKELRNAI SKNKIDKPM YVYYFESPEK FAFNKVIRTE NQNEISLEKF NEFKETIQNK LFKQDGFKDI SLYEPGKGDE KPTPLLMHLK L PRNTGMLP YTNTNNVSTL IEQGYSIKID KIVRIVIDGK HYIKAEASVV SSLDFKDDVS KGDSWGKANY NDWSNKLTPN EL ADVNDYM RGGYTAINNY LISNGPVNNP NPELDSKITN IENALKREPI PTNLTVYRRS GPQEFGLTLT SPEYDFNKLE NID AFKSKW EGQALSYPNF ISTSIGSVNM SAFAKRKIVL RITIPKGSPG AYLSAIPGYA GEYEVLLNHG SKFKINKIDS YKDG TITKL IVDATLIPEN LYFQGLEHHH HHH UniProtKB: ADP-ribosyltransferase enzymatic component |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 21 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.58 mg/mL |
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Buffer | pH: 7.5 Details: 10 mM HEPES (pH 7.5), 1 mM CaCl2, and 0.003% (w/v) LMNG |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11284 / Average exposure time: 3.36 sec. / 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: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |