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- PDB-6j0f: Cryo-EM Structure of an Extracellular Contractile Injection Syste... -

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Basic information

Entry
Database: PDB / ID: 6j0f
TitleCryo-EM Structure of an Extracellular Contractile Injection System, PVC sheath/tube terminator in extended state
Components
  • Pvc1
  • Pvc16
KeywordsPROTEIN TRANSPORT / assembly / Photorhabdus asymbiotica / PVC / contractile injection system / bacteriophage-like
Function / homologyPvc16, N-terminal / Pvc16 N-terminal domain / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / structural molecule activity / Uncharacterized protein / Conserved hypothetical phage tail region protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica subsp. asymbiotica (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsJiang, F. / Li, N. / Wang, X. / Cheng, J. / Huang, Y. / Yang, Y. / Yang, J. / Cai, B. / Wang, Y. / Jin, Q. / Gao, N.
CitationJournal: Cell / Year: 2019
Title: Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System.
Authors: Feng Jiang / Ningning Li / Xia Wang / Jiaxuan Cheng / Yaoguang Huang / Yun Yang / Jianguo Yang / Bin Cai / Yi-Ping Wang / Qi Jin / Ning Gao /
Abstract: Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of ...Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea. Here, we report the cryo-EM structure of an intact PVC from P. asymbiotica. This over 10-MDa device resembles a simplified T4 phage tail, containing a hexagonal baseplate complex with six fibers and a capped 117-nanometer sheath-tube trunk. One distinct feature of the PVC is the presence of three variants for both tube and sheath proteins, indicating a functional specialization of them during evolution. The terminal hexameric cap docks onto the topmost layer of the inner tube and locks the outer sheath in pre-contraction state with six stretching arms. Our results on the PVC provide a framework for understanding the general mechanism of widespread CISs and pave the way for using them as delivery tools in biological or therapeutic applications.
History
DepositionDec 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Pvc16
B: Pvc16
C: Pvc16
D: Pvc16
E: Pvc16
F: Pvc16
a: Pvc1
b: Pvc1
c: Pvc1
d: Pvc1
e: Pvc1
f: Pvc1


Theoretical massNumber of molelcules
Total (without water)293,43612
Polymers293,43612
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Pvc16


Mass: 32373.434 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77 / Gene: PAU_03338, PA-RVA20-21-0156 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VNM9
#2: Protein
Pvc1


Mass: 16532.557 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77 / Gene: PAU_03353, PA-RVA20-21-0171 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VNP4

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: sheath/tube terminator and the last layer of tube in contracted state
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Photorhabdus asymbiotica (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 46.4 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45000 / Symmetry type: POINT

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