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- PDB-6rao: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6... -

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Basic information

Entry
Database: PDB / ID: 6rao
TitleCryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
Components
  • Afp1
  • Afp11
  • Afp12
  • Afp2
  • Afp3
  • Afp4
  • Afp5
  • Afp7
  • Afp9
KeywordsVIRUS LIKE PARTICLE / Anti-feeding prophage / secretion system / AFP / contractile
Function / homology
Function and homology information


virus tail / structural molecule activity
Similarity search - Function
: / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain ...: / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Afp12 / Afp11 / Afp9 / Afp7 / Afp5 / Afp4 / Afp3 / Afp2 / Afp1
Similarity search - Component
Biological speciesSerratia entomophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDesfosses, A.
CitationJournal: 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
DepositionApr 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author / em_image_scans
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Afp1
B: Afp1
C: Afp2
D: Afp3
F: Afp5
H: Afp9
E: Afp4
G: Afp7
I: Afp11
J: Afp12


Theoretical massNumber of molelcules
Total (without water)398,23910
Polymers398,23910
Non-polymers00
Water0
1
A: Afp1
B: Afp1
C: Afp2
D: Afp3
F: Afp5
H: Afp9
E: Afp4
G: Afp7
I: Afp11
J: Afp12
x 6


Theoretical massNumber of molelcules
Total (without water)2,389,43760
Polymers2,389,43760
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation5
MethodPISA

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Components

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Protein , 9 types, 10 molecules ABCDFHEGIJ

#1: Protein Afp1


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 Afp2


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 Afp3


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 Afp5


Mass: 17026.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD4
#5: Protein Afp9


Mass: 15693.884 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD0
#6: Protein Afp4


Mass: 45565.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD5
#7: Protein Afp7


Mass: 25259.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAD2
#8: Protein Afp11


Mass: 67327.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAC8
#9: Protein Afp12


Mass: 106905.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Gene: afp12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6HAC7

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
Type: COMPLEX
Details: Note that the needle is not resolved here because of 6-fold symmetry imposition
Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Serratia entomophila (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46991 / Algorithm: BACK PROJECTION / Symmetry type: POINT

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