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- EMDB-4871: Cryo-EM structure of the anti-feeding prophage (AFP) needle from ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4871 | |||||||||
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Title | Cryo-EM structure of the anti-feeding prophage (AFP) needle from signal-subtracted particles | |||||||||
![]() | Cryo-EM structure of the anti-feeding prophage (AFP) needle from signal-subtracted particles | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Desfosses A | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.4 KB | Display | ![]() |
Images | ![]() | 82.6 KB | ||
Others | ![]() ![]() | 17 MB 17 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 362.7 KB | Display | ![]() |
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Full document | ![]() | 361.9 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4782C ![]() 4783C ![]() 4784C ![]() 4800C ![]() 4801C ![]() 4802C ![]() 4803C ![]() 4859C ![]() 4876C ![]() 6raoC ![]() 6rapC ![]() 6rbkC ![]() 6rbnC ![]() 6rc8C ![]() 6rglC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the anti-feeding prophage (AFP) needle from signal-subtracted particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Half map: None
File | emd_4871_half_map_1.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_4871_half_map_2.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of the anti-feeding prophage (AFP) helical shea...
Entire | Name: Cryo-EM structure of the anti-feeding prophage (AFP) helical sheath-tube complex in extended state |
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Components |
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-Supramolecule #1: Cryo-EM structure of the anti-feeding prophage (AFP) helical shea...
Supramolecule | Name: Cryo-EM structure of the anti-feeding prophage (AFP) helical sheath-tube complex in extended state 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: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |