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Yorodumi- PDB-6j0n: Cryo-EM Structure of an Extracellular Contractile Injection Syste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j0n | ||||||
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Title | Cryo-EM Structure of an Extracellular Contractile Injection System, baseplate in extended state, refined in C6 symmetry | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / assembly / Photorhabdus asymbiotica / PVC / contractile injection system / bacteriophage-like | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Photorhabdus asymbiotica subsp. asymbiotica (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Jiang, F. / Li, N. / Wang, X. / Cheng, J. / Huang, Y. / Yang, Y. / Yang, J. / Cai, B. / Wang, Y. / Jin, Q. / Gao, N. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6j0n.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6j0n.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6j0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j0n_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6j0n_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6j0n_validation.xml.gz | 428.8 KB | Display | |
Data in CIF | 6j0n_validation.cif.gz | 642 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/6j0n ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j0n | HTTPS FTP |
-Related structure data
Related structure data | 9765MC 9760C 9761C 9762C 9763C 9764C 6j0bC 6j0cC 6j0fC 6j0mC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Protein , 9 types, 54 molecules DEFGHIJKLMNOPQRSTUVWXYZabcdefg...
#1: Protein | Mass: 15990.021 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_03345, PA-RVA20-21-0163 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VNN6 #2: Protein | Mass: 82807.523 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_03343, PA-RVA20-21-0161 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VNN4 #3: Protein | Mass: 107761.789 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_03342, PA-RVA20-21-0160 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VNN3 #4: Protein | Mass: 45866.652 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_03350, PA-RVA20-21-0168 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VNP1 #5: Protein | Mass: 25336.664 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_03347, PA-RVA20-21-0165 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VNN8 #6: Protein | Mass: 39374.281 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_03352, PA-RVA20-21-0170 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VNP3 #7: Protein | Mass: 17506.895 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_03349, PA-RVA20-21-0167 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VNP0 #8: Protein | 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 #9: Protein | Mass: 48794.949 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_03351, PA-RVA20-21-0169 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VNP2 |
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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: baseplate in extended state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Photorhabdus asymbiotica (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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 / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 46.4 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C6 (6 fold cyclic) |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63000 / Symmetry type: POINT |