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- PDB-9qgn: Cryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in ... -

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Basic information

Entry
Database: PDB / ID: 9qgn
TitleCryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in extended state
Components
  • DUF4255 domain-containing protein
  • Phage tail protein
  • Phage tail sheath family protein
KeywordsVIRUS LIKE PARTICLE / Contractile injection system
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Pvc16, N-terminal / Pvc16 N-terminal domain / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Phage tail sheath family protein / Phage tail protein / DUF4255 domain-containing protein
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsMarin-Arraiza, L. / Taylor, N.M.I.
Funding support Denmark, Spain, 5items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Novo Nordisk FoundationNNF17OC0031006 Denmark
Novo Nordisk FoundationNNF23OC0081528 Denmark
LundbeckfondenR434-2023-289 Denmark
La Caixa FoundationLCF/BQ/EU21/11890147 Spain
CitationJournal: Nat Commun / Year: 2025
Title: Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states.
Authors: Leyre Marín-Arraiza / Aritz Roa-Eguiara / Tillmann Pape / Nicholas Sofos / Ivo Alexander Hendriks / Michael Lund Nielsen / Eva Maria Steiner-Rebrova / Nicholas M I Taylor /
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 ...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.
History
DepositionMar 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF4255 domain-containing protein
B: DUF4255 domain-containing protein
C: DUF4255 domain-containing protein
D: DUF4255 domain-containing protein
E: DUF4255 domain-containing protein
F: DUF4255 domain-containing protein
1A: Phage tail protein
1B: Phage tail protein
1C: Phage tail protein
1D: Phage tail protein
1E: Phage tail protein
1F: Phage tail protein
1G: Phage tail protein
1H: Phage tail protein
1I: Phage tail protein
1J: Phage tail protein
1K: Phage tail protein
1L: Phage tail protein
2A: Phage tail sheath family protein
2B: Phage tail sheath family protein
2C: Phage tail sheath family protein
2D: Phage tail sheath family protein
2E: Phage tail sheath family protein
2F: Phage tail sheath family protein


Theoretical massNumber of molelcules
Total (without water)632,75124
Polymers632,75124
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
DUF4255 domain-containing protein


Mass: 33299.473 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc16 - cap protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18165 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JUZ8
#2: Protein
Phage tail protein


Mass: 16574.574 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: Pvc1 - tube protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18090 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JSR5
#3: Protein
Phage tail sheath family protein


Mass: 39009.828 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc2 - sheath protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18095 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JN00
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PlPVC cap (C6) in extended state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionDetails: Patch CTF Estimation in cryoSPARC, fit local CTF to micrograph, including tilted, bent, deformed samples)
Type: NONE
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57353 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00244358
ELECTRON MICROSCOPYf_angle_d0.41960552
ELECTRON MICROSCOPYf_dihedral_angle_d3.6695932
ELECTRON MICROSCOPYf_chiral_restr0.0447044
ELECTRON MICROSCOPYf_plane_restr0.0037854

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