6J0N image
Deposition Date 2018-12-25
Release Date 2019-04-10
Last Version Date 2024-03-27
Entry Detail
PDB ID:
6J0N
Keywords:
PROTEIN TRANSPORT
Title:
Cryo-EM Structure of an Extracellular Contractile Injection System, baseplate in extended state, refined in C6 symmetry
Biological Source:
Source Organism:
Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (Taxon ID: 553480)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6J0N validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pvc1
Gene (Uniprot):PA-RVA20-21-0171
Chain IDs:QA (auth: 1), RA (auth: 2), SA (auth: 3), TA (auth: 4), UA (auth: 5), BB (auth: z)
Chain Length:149
Number of Molecules:6
Biological Source:Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)
UniProt ID:B6VNP4 Pfam ID:PF06841
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pvc9
Gene (Uniprot):PA-RVA20-21-0163
Chain IDs:A (auth: D), B (auth: E), C (auth: F), D (auth: G), E (auth: H), F (auth: I)
Chain Length:140
Number of Molecules:6
Biological Source:Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)
UniProt ID:B6VNN6 Pfam ID:PF04965
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pvc11
Gene (Uniprot):PA-RVA20-21-0161
Chain IDs:G (auth: J), H (auth: K), I (auth: L), J (auth: M), K (auth: N), L (auth: O)
Chain Length:355
Number of Molecules:6
Biological Source:Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)
UniProt ID:B6VNN4
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pvc12
Gene (Uniprot):PA-RVA20-21-0160
Chain IDs:M (auth: P), N (auth: Q), O (auth: R), P (auth: S), Q (auth: T), R (auth: U)
Chain Length:152
Number of Molecules:6
Biological Source:Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)
UniProt ID:B6VNN3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pvc4
Gene (Uniprot):PA-RVA20-21-0168
Chain IDs:S (auth: V), T (auth: W), U (auth: X), V (auth: Y), W (auth: Z), X (auth: a)
Chain Length:410
Number of Molecules:6
Biological Source:Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)
UniProt ID:B6VNP1 Pfam ID:PF17482
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pvc7
Gene (Uniprot):PA-RVA20-21-0165
Chain IDs:Y (auth: b), Z (auth: c), AA (auth: d), BA (auth: e), CA (auth: f), DA (auth: g)
Chain Length:229
Number of Molecules:6
Biological Source:Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)
UniProt ID:B6VNN8 Pfam ID:PF19266
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pvc2
Gene (Uniprot):PA-RVA20-21-0170
Chain IDs:EA (auth: h), FA (auth: i), GA (auth: j), HA (auth: k), IA (auth: l), JA (auth: m)
Chain Length:140
Number of Molecules:6
Biological Source:Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)
UniProt ID:B6VNP3 Pfam ID:PF04984, PF17482
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pvc5
Gene (Uniprot):PA-RVA20-21-0167
Chain IDs:KA (auth: n), LA (auth: o), MA (auth: p), NA (auth: q), OA (auth: r), PA (auth: s)
Chain Length:152
Number of Molecules:6
Biological Source:Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)
UniProt ID:B6VNP0 Pfam ID:PF06841
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pvc3
Gene (Uniprot):PA-RVA20-21-0169
Chain IDs:VA (auth: t), WA (auth: u), XA (auth: v), YA (auth: w), ZA (auth: x), AB (auth: y)
Chain Length:950
Number of Molecules:6
Biological Source:Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)
UniProt ID:B6VNP2 Pfam ID:PF04984, PF17482
Ligand Molecules
NA
Primary Citation
Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System.
Cell 177 370 383.e15 (2019)
PMID: 30905475 DOI: 10.1016/j.cell.2019.02.020

Abstact

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.

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Primary Citation of related structures
6J0N