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Yorodumi- EMDB-4801: Cryo-EM structure of the anti-feeding prophage cap (AFP tube term... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4801 | |||||||||
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Title | Cryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap), ending with Afp3 | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Serratia entomophila (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Desfosses A | |||||||||
Citation | Journal: Nat Microbiol / Year: 2019 Title: Atomic structures of an entire contractile injection system in both the extended and contracted states. Authors: Ambroise Desfosses / Hariprasad Venugopal / Tapan Joshi / Jan Felix / Matthew Jessop / Hyengseop Jeong / Jaekyung Hyun / J Bernard Heymann / Mark R H Hurst / Irina Gutsche / Alok K Mitra / Abstract: Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. Although the number of atomic-resolution insights into contractile bacteriophage tails, ...Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. Although the number of atomic-resolution insights into contractile bacteriophage tails, bacterial type six secretion systems and R-pyocins is rapidly increasing, structural information on the contraction of bacterial phage-like protein-translocation structures directed towards eukaryotic hosts is scarce. Here, we characterize the antifeeding prophage AFP from Serratia entomophila by cryo-electron microscopy. We present the high-resolution structure of the entire AFP particle in the extended state, trace 11 protein chains de novo from the apical cap to the needle tip, describe localization variants and perform specific structural comparisons with related systems. We analyse inter-subunit interactions and highlight their universal conservation within contractile injection systems while revealing the specificities of AFP. Furthermore, we provide the structure of the AFP sheath-baseplate complex in a contracted state. This study reveals atomic details of interaction networks that accompany and define the contraction mechanism of toxin-delivery tailocins, offering a comprehensive framework for understanding their mode of action and for their possible adaptation as biocontrol agents. | |||||||||
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_4801.map.gz | 18.8 MB | EMDB map data format | |
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Header (meta data) | emd-4801-v30.xml emd-4801.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4801_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_4801.png | 138.1 KB | ||
Others | emd_4801_half_map_1.map.gz emd_4801_half_map_2.map.gz | 97.1 MB 97.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4801 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4801 | HTTPS FTP |
-Validation report
Summary document | emd_4801_validation.pdf.gz | 274.6 KB | Display | EMDB validaton report |
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Full document | emd_4801_full_validation.pdf.gz | 273.8 KB | Display | |
Data in XML | emd_4801_validation.xml.gz | 12.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4801 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4801 | HTTPS FTP |
-Related structure data
Related structure data | 4782C 4783C 4784C 4800C 4802C 4803C 4859C 4871C 4876C 6raoC 6rapC 6rbkC 6rbnC 6rc8C 6rglC 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_4801.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 4801 half map 1.map
File | emd_4801_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 4801 half map 2.map
File | emd_4801_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of the anti-feeding prophage cap (AFP tube term...
Entire | Name: Cryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap), ending with Afp3 |
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Components |
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-Supramolecule #1: Cryo-EM structure of the anti-feeding prophage cap (AFP tube term...
Supramolecule | Name: Cryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap), ending with Afp3 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: A scaling by a factor of 2 is recommended for visualisation |
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Source (natural) | Organism: Serratia entomophila (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |