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Yorodumi- EMDB-42279: Cryo-EM of Vibrio cholerae toxin co-regulated pilus - asymmetric ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42279 | |||||||||
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Title | Cryo-EM of Vibrio cholerae toxin co-regulated pilus - asymmetric reconstruction | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Toxin / Cholera / Type IV pilus / CELL ADHESION | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Sonani RR / Kundra S / Craig L / Egelman EH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Tad and toxin-coregulated pilus structures reveal unexpected diversity in bacterial type IV pili. Authors: Ravi R Sonani / Juan Carlos Sanchez / Joseph K Baumgardt / Shivani Kundra / Elizabeth R Wright / Lisa Craig / Edward H Egelman / Abstract: Type IV pili (T4P) are ubiquitous in both bacteria and archaea. They are polymers of the major pilin protein, which has an extended and protruding N-terminal helix, α1, and a globular C-terminal ...Type IV pili (T4P) are ubiquitous in both bacteria and archaea. They are polymers of the major pilin protein, which has an extended and protruding N-terminal helix, α1, and a globular C-terminal domain. Cryo-EM structures have revealed key differences between the bacterial and archaeal T4P in their C-terminal domain structure and in the packing and continuity of α1. This segment forms a continuous α-helix in archaeal T4P but is partially melted in all published bacterial T4P structures due to a conserved helix breaking proline at position 22. The tad (tight adhesion) T4P are found in both bacteria and archaea and are thought to have been acquired by bacteria through horizontal transfer from archaea. Tad pilins are unique among the T4 pilins, being only 40 to 60 residues in length and entirely lacking a C-terminal domain. They also lack the Pro22 found in all high-resolution bacterial T4P structures. We show using cryo-EM that the bacterial tad pilus from is composed of continuous helical subunits that, like the archaeal pilins, lack the melted portion seen in other bacterial T4P and share the packing arrangement of the archaeal T4P. We further show that a bacterial T4P, the toxin coregulated pilus, which lacks Pro22 but is not in the tad family, has a continuous N-terminal α-helix, yet its α1 s are arranged similar to those in other bacterial T4P. Our results highlight the role of Pro22 in helix melting and support an evolutionary relationship between tad and archaeal T4P. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42279.map.gz | 53.6 MB | EMDB map data format | |
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Header (meta data) | emd-42279-v30.xml emd-42279.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42279_fsc.xml | 8.3 KB | Display | FSC data file |
Images | emd_42279.png | 61 KB | ||
Filedesc metadata | emd-42279.cif.gz | 4.8 KB | ||
Others | emd_42279_half_map_1.map.gz emd_42279_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42279 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42279 | HTTPS FTP |
-Related structure data
Related structure data | 8uhfMC 8u1kC 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_42279.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: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_42279_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42279_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Toxin co-regulated pilus
Entire | Name: Toxin co-regulated pilus |
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Components |
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-Supramolecule #1: Toxin co-regulated pilus
Supramolecule | Name: Toxin co-regulated pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
-Macromolecule #1: Toxin co-regulated pilin
Macromolecule | Name: Toxin co-regulated pilin / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 20.275205 KDa |
Sequence | String: MTLLEVIIVL GIMGVVSAGV VTLAQRAIDS QNMTKAAQSL NSIQVALTQT YRGLGNYPAT ADATAASKLT SGLVSLGKIS SDEAKNPFI GTNMNIFSFP RNAAANKAFA ISVDGLTQAQ CKTLITSVGD MFPYIAIKAG GAVALADLGD FENSAAAAET G VGVIKSIA ...String: MTLLEVIIVL GIMGVVSAGV VTLAQRAIDS QNMTKAAQSL NSIQVALTQT YRGLGNYPAT ADATAASKLT SGLVSLGKIS SDEAKNPFI GTNMNIFSFP RNAAANKAFA ISVDGLTQAQ CKTLITSVGD MFPYIAIKAG GAVALADLGD FENSAAAAET G VGVIKSIA PASKNLDLTN ITAVEKLCKG TAPFGVAFGN S UniProtKB: Toxin co-regulated pilin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |