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- EMDB-9760: Cryo-EM Structure of an Extracellular Contractile Injection Syste... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9760 | |||||||||
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Title | Cryo-EM Structure of an Extracellular Contractile Injection System, PVC sheath-tube complex in extended state | |||||||||
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![]() | assembly / Photorhabdus asymbiotica / PVC / contractile injection system / bacteriophage-like / PROTEIN TRANSPORT | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Jiang F / Li N | |||||||||
![]() | ![]() 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 |
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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 | ![]() | 14.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11 KB 11 KB | Display Display | ![]() |
Images | ![]() | 245 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 515.9 KB | Display | ![]() |
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Full document | ![]() | 515.5 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j0bMC ![]() 9761C ![]() 9762C ![]() 9763C ![]() 9764C ![]() 9765C ![]() 6j0cC ![]() 6j0fC ![]() 6j0mC ![]() 6j0nC M: atomic model generated by this map 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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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.121 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : sheath and tube in extended state
Entire | Name: sheath and tube in extended state |
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Components |
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-Supramolecule #1: sheath and tube in extended state
Supramolecule | Name: sheath and tube in extended state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Pvc2
Macromolecule | Name: Pvc2 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 43949 / 3105-77 |
Molecular weight | Theoretical: 39.374281 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTTVTSYPGV YIEELNSLAL SVSNSATAVP VFAVDEQNQY ISEDNAIRIN SWMDYLNLIG NFNNEDKLDV SVRAYFANGG GYCYLVKTT SLEKIIPTLD DVTLLVAAGE DIKTTVDVLC QPGKGLFAVF DGPETELTIN GAEEAKQAYT ATPFAAVYYP W LKADWANI ...String: MTTVTSYPGV YIEELNSLAL SVSNSATAVP VFAVDEQNQY ISEDNAIRIN SWMDYLNLIG NFNNEDKLDV SVRAYFANGG GYCYLVKTT SLEKIIPTLD DVTLLVAAGE DIKTTVDVLC QPGKGLFAVF DGPETELTIN GAEEAKQAYT ATPFAAVYYP W LKADWANI DIPPSAVMAG VYASVDLSRG VWKAPANVAL KGGLEPKFLV TDELQGEYNT GRAINMIRNF SNTGTTVWGA RT LEDKDNW RYVPVRRLFN SVERDIKRAM SFAMFEPNNQ PTWERVRAAI SNYLYSLWQQ GGLAGSKEED AYFVQIGKGI TMT QEQIDA GQMIVKVGLA AVRPAEFIIL QFTQDVEQR UniProtKB: Phage tail sheath protein |
-Macromolecule #2: Pvc1
Macromolecule | Name: Pvc1 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 43949 / 3105-77 |
Molecular weight | Theoretical: 16.532557 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSTSTSQIAV EYPIPVYRFI VSVGDEKIPF NSVSGLDISY DTIEYRDGVG NWFKMPGQSQ STNITLRKGV FPGKTELFDW INSIQLNQV EKKDITISLT NDAGTELLMT WNVSNAFPTS LTSPSFDATS NDIAVQEITL MADRVIMQAV UniProtKB: Conserved hypothetical phage tail region protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 46.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 39.3 Å Applied symmetry - Helical parameters - Δ&Phi: 19.9 ° Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 551000 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |