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Yorodumi- PDB-6rap: Cryo-EM structure of the anti-feeding prophage cap (AFP tube term... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rap | ||||||
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Title | Cryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap) | ||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / Anti-feeding prophage / secretion system / AFP / contractile / cap / tube terminating protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Serratia entomophila (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6rap.cif.gz | 229.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rap.ent.gz | 182.8 KB | Display | PDB format |
PDBx/mmJSON format | 6rap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rap_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6rap_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6rap_validation.xml.gz | 50.2 KB | Display | |
Data in CIF | 6rap_validation.cif.gz | 75.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/6rap ftp://data.pdbj.org/pub/pdb/validation_reports/ra/6rap | HTTPS FTP |
-Related structure data
Related structure data | 4784MC 4782C 4783C 4800C 4801C 4802C 4803C 4859C 4871C 4876C 6raoC 6rbkC 6rbnC 6rc8C 6rglC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 16449.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD8 #2: Protein | | Mass: 38784.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD7 #3: Protein | | Mass: 48777.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD6 #4: Protein | | Mass: 32250.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAC3 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap) Type: COMPLEX Details: A scaling by a factor of 2 is recommended for visualisation Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Serratia entomophila (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Particle selection | Num. of particles selected: 30858 | ||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23797 / Symmetry type: POINT |