+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0088 | |||||||||
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Title | XaxAB pore complex from Xenorhabdus nematophila | |||||||||
Map data | ||||||||||
Sample |
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Keywords | bacterial toxin / pore forming-toxins / TOXIN | |||||||||
Function / homology | : / membrane / XaxA / XaxB Function and homology information | |||||||||
Biological species | Xenorhabdus nematophila ATCC 19061 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Schubert E / Vetter IR / Prumbaum D / Penczek PA / Raunser S | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Elife / Year: 2018 Title: Membrane insertion of α-xenorhabdolysin in near-atomic detail. Authors: Evelyn Schubert / Ingrid R Vetter / Daniel Prumbaum / Pawel A Penczek / Stefan Raunser / Abstract: α-Xenorhabdolysins (Xax) are α-pore-forming toxins (α-PFT) that form 1-1.3 MDa large pore complexes to perforate the host cell membrane. PFTs are used by a variety of bacterial pathogens to attack ...α-Xenorhabdolysins (Xax) are α-pore-forming toxins (α-PFT) that form 1-1.3 MDa large pore complexes to perforate the host cell membrane. PFTs are used by a variety of bacterial pathogens to attack host cells. Due to the lack of structural information, the molecular mechanism of action of Xax toxins is poorly understood. Here, we report the cryo-EM structure of the XaxAB pore complex from and the crystal structures of the soluble monomers of XaxA and XaxB. The structures reveal that XaxA and XaxB are built similarly and appear as heterodimers in the 12-15 subunits containing pore, classifying XaxAB as bi-component α-PFT. Major conformational changes in XaxB, including the swinging out of an amphipathic helix are responsible for membrane insertion. XaxA acts as an activator and stabilizer for XaxB that forms the actual transmembrane pore. Based on our results, we propose a novel structural model for the mechanism of Xax intoxication. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0088.map.gz | 14.3 MB | EMDB map data format | |
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Header (meta data) | emd-0088-v30.xml emd-0088.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_0088.png | 141.2 KB | ||
Filedesc metadata | emd-0088.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0088 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0088 | HTTPS FTP |
-Validation report
Summary document | emd_0088_validation.pdf.gz | 232.8 KB | Display | EMDB validaton report |
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Full document | emd_0088_full_validation.pdf.gz | 232 KB | Display | |
Data in XML | emd_0088_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0088 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0088 | HTTPS FTP |
-Related structure data
Related structure data | 6gy6MC 6gy7C 6gy8C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0088.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : XaxAB complex (13 XaxA + 13 XaxB)
Entire | Name: XaxAB complex (13 XaxA + 13 XaxB) |
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Components |
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-Supramolecule #1: XaxAB complex (13 XaxA + 13 XaxB)
Supramolecule | Name: XaxAB complex (13 XaxA + 13 XaxB) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Xenorhabdus nematophila ATCC 19061 (bacteria) |
-Supramolecule #2: XaxA protomer
Supramolecule | Name: XaxA protomer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: 13 XaxA protomers in the XaxAB pore complex |
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Source (natural) | Organism: Xenorhabdus nematophila ATCC 19061 (bacteria) |
-Supramolecule #3: XaxB protomer
Supramolecule | Name: XaxB protomer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: 13 XaxB protomers in the XaxAB pore complex |
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Source (natural) | Organism: Xenorhabdus nematophila ATCC 19061 (bacteria) |
-Macromolecule #1: XaxA
Macromolecule | Name: XaxA / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenorhabdus nematophila ATCC 19061 (bacteria) |
Molecular weight | Theoretical: 47.465859 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MENDMSSNQT LAEKKIPVSE VPSATLKMLT SQAEGVARPG GIFTKGDLIN IKLYVKHSLE LPFTLEGVKE YIGYNDIDID GLKPAKMAT LFKEIHDHAL SWSGVESKVQ QQSIDLENAG KQITLTGDEI ISVIDQMPII ERVKNKLGDL TDKQLAEITY T NDDKEIAV ...String: MENDMSSNQT LAEKKIPVSE VPSATLKMLT SQAEGVARPG GIFTKGDLIN IKLYVKHSLE LPFTLEGVKE YIGYNDIDID GLKPAKMAT LFKEIHDHAL SWSGVESKVQ QQSIDLENAG KQITLTGDEI ISVIDQMPII ERVKNKLGDL TDKQLAEITY T NDDKEIAV ELGNILESMK KDIKRQQENT QKVKTAVSDF KLKLIGGELS DGTIAQGLQP QISSKKKLMD DNNLSTTIKD LQ SKIDEKN KEIDQFQKDY NKYVGLAFSG MVGGIISWAI TGGIFGDKAE KARKQKNKLI DEVKDLQSQV KDKSALQTSV QNL SLSFAG IHTSMVDAEE ALNHLDFMWN TMLTQITTSR DKFDDINDAL KLTSFVIAFK QVIEPWRDVQ GSAAQLIQTF DEAL AEYKK LYHGTLEVLF QGPHHHHHH UniProtKB: XaxA |
-Macromolecule #2: XaxB
Macromolecule | Name: XaxB / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenorhabdus nematophila ATCC 19061 (bacteria) |
Molecular weight | Theoretical: 38.518688 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: YPEINIKAMN QAVNTIWLLA QRQTSGIEII NDKVKRISAY SREFDEMMRD SLAQLAPVLK QLTSDAAFQT IAQIDEALAD PSLSKDDRE ALTLERNNLI QNLSKHIDNV IVSFTGRTSK LTNKISDISD MVIAERLQDL VTQTESQKTE LQSDIDPKTE K RNKLDADR ...String: YPEINIKAMN QAVNTIWLLA QRQTSGIEII NDKVKRISAY SREFDEMMRD SLAQLAPVLK QLTSDAAFQT IAQIDEALAD PSLSKDDRE ALTLERNNLI QNLSKHIDNV IVSFTGRTSK LTNKISDISD MVIAERLQDL VTQTESQKTE LQSDIDPKTE K RNKLDADR EKIIESQDVI RQNNIADMFK DFIPSAKDID GLDFTQPKKE AIKQAIKQGA EIARKILGKV SEGLKYIDLA DA RMKLSDQ IDQLITETDE LKAKIREVEL RLSGLKDVMQ IDTERTTLLT EAVKIEQVWI SFAEQLHKLS NDEINQQDLS NLI NGQLDF LNNLTLQYNK LK UniProtKB: XaxB |
-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: 7.5 |
Grid | Model: C-flat-2/1 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298.15 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |