9QGL | pdb_00009qgl

Cryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6), in extended state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states.

Marin-Arraiza, L.Roa-Eguiara, A.Pape, T.Sofos, N.Hendriks, I.A.Lund Nielsen, M.Steiner-Rebrova, E.M.Taylor, N.M.I.

(2025) Nat Commun 16: 9327-9327

  • DOI: https://doi.org/10.1038/s41467-025-64377-z
  • Primary Citation of Related Structures:  
    9QGL, 9QGM, 9QGN, 9QGO, 9QGP

  • PubMed Abstract: 

    Contractile injection systems (CISs) are phage tail-like nanosyringes that mediate bacterial interactions by puncturing target cell membranes. Within these systems, Photorhabdus Virulence Cassettes (PVCs) can translocate toxins across eukaryotic target cell membranes and have been engineered to deliver diverse protein cargoes into non-natively-targeted organisms. Despite the structural insights into several CISs, including one PVC from P. asymbiotica, information on PVCs from other species and details on the contraction mechanism remain limited. Here, we present the single-particle cryo-electron microscopy structure of PlPVC1, a PVC from the nematode symbiont and insect pathogen Photorhabdus luminescens DJC, in both extended and contracted states. This particle displays distinct structural features that differ from other CISs, such as a cage surrounding the central spike, a larger sheath adaptor, and a plug exposed to the tube lumen. Moreover, we present the structures of the PlPVC1 fiber and the baseplate of the contracted particle, yielding insight into the contraction mechanism. This study provides structural details of the extended and contracted states of the PlPVC1 particle and supports the model in which contraction is triggered. Furthermore, it facilitates the comparison of PlPVC1 with other CISs and expands the scope of engineering opportunities for future biomedical and biotechnological applications.


  • Organizational Affiliation
    • Novo Nordisk Foundation Center for Protein Research, ICMM, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phage tail protein149Photorhabdus luminescensMutation(s): 0 
Gene Names: GPY51_18090
UniProt
Find proteins for A0A6L9JSR5 (Photorhabdus laumondii subsp. laumondii)
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UniProt GroupA0A6L9JSR5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phage tail sheath family protein354Photorhabdus luminescensMutation(s): 0 
Gene Names: GPY51_18095
UniProt
Find proteins for A0A6L9JN00 (Photorhabdus laumondii subsp. laumondii)
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UniProt GroupA0A6L9JN00
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phage tail protein152Photorhabdus luminescensMutation(s): 0 
Gene Names: C6H66_14800
UniProt
Find proteins for A0A2S8PZE9 (Photorhabdus hindustanensis)
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UniProt GroupA0A2S8PZE9
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Contractile injection system tube protein N-terminal domain-containing protein227Photorhabdus luminescensMutation(s): 0 
Gene Names: C6H66_14790
UniProt
Find proteins for A0A2S8PZG1 (Photorhabdus hindustanensis)
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UniProt GroupA0A2S8PZG1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17239Photorhabdus luminescensMutation(s): 0 
Gene Names: plu1722
UniProt
Find proteins for Q7MB49 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17905Photorhabdus luminescensMutation(s): 0 
Gene Names: plu1720
UniProt
Find proteins for Q7N649 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Baseplate protein J-like domain-containing protein966Photorhabdus luminescensMutation(s): 0 
Gene Names: GPY51_18145
UniProt
Find proteins for A0A6L9JN06 (Photorhabdus laumondii subsp. laumondii)
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UniProt GroupA0A6L9JN06
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Phage tail sheath family protein466Photorhabdus luminescensMutation(s): 0 
Gene Names: GPY51_18100
UniProt
Find proteins for A0A6L9JMV2 (Photorhabdus laumondii subsp. laumondii)
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UniProt GroupA0A6L9JMV2
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Phage tail sheath family protein392Photorhabdus luminescensMutation(s): 0 
Gene Names: GPY51_18105
UniProt
Find proteins for A0A6L9JN29 (Photorhabdus laumondii subsp. laumondii)
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UniProt GroupA0A6L9JN29
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF14CC0001
Novo Nordisk FoundationDenmarkNNF17OC0031006
Novo Nordisk FoundationDenmarkNNF23OC0081528
LundbeckfondenDenmarkR434-2023-289
La Caixa FoundationSpainLCF/BQ/EU21/11890147

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Data collection, Database references