9QGO | pdb_00009qgo

Interaction between PlPVC1 baseplate and fiber in extended state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tail fiber protein
A, B, C
434Photorhabdus luminescensMutation(s): 0 
Gene Names: GPY51_18150
UniProt
Find proteins for A0A6L9JMW1 (Photorhabdus laumondii subsp. laumondii)
Explore A0A6L9JMW1 
Go to UniProtKB:  A0A6L9JMW1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6L9JMW1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Baseplate protein J-like domain-containing proteinD [auth a],
E [auth b],
F [auth c]
966Photorhabdus luminescensMutation(s): 0 
Gene Names: GPY51_18145
UniProt
Find proteins for A0A6L9JN06 (Photorhabdus laumondii subsp. laumondii)
Explore A0A6L9JN06 
Go to UniProtKB:  A0A6L9JN06
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6L9JN06
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5109:

Structure Validation

View Full Validation Report



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