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- EMDB-53143: Cryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6... -

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Entry
Database: EMDB / ID: EMD-53143
TitleCryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6), in contracted state
Map dataCryo-EM structure of the PlPVC baseplate, 6-fold symmetrized, in contracted state
Sample
  • Complex: Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized (C6), in contracted state
Keywordscontractile injection system / VIRUS LIKE PARTICLE
Biological speciesPhotorhabdus luminescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsMarin-Arraiza L / Taylor NMI
Funding support Denmark, Spain, 5 items
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, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53143.png

Downloads & links

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Map

FileDownload / File: emd_53143.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the PlPVC baseplate, 6-fold symmetrized, in contracted state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 700 pix.
= 840. Å		1.2 Å/pix.
x 700 pix.
= 840. Å		1.2 Å/pix.
x 700 pix.
= 840. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.6224463 - 1.53696
Average (Standard dev.)-0.0002505408 (±0.043029357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 840.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53143_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized,...

Fileemd_53143_additional_1.map
AnnotationCryo-EM structure of the PlPVC baseplate, 6-fold symmetrized, in contracted state - filtered to 10 angstrom
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized,...

Fileemd_53143_half_map_1.map
AnnotationCryo-EM structure of the PlPVC baseplate, 6-fold symmetrized, in contracted state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized,...

Fileemd_53143_half_map_2.map
AnnotationCryo-EM structure of the PlPVC baseplate, 6-fold symmetrized, in contracted state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized (C6)...

EntireName: Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized (C6), in contracted state
Components
  • Complex: Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized (C6), in contracted state

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Supramolecule #1: Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized (C6)...

SupramoleculeName: Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized (C6), in contracted state
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Photorhabdus luminescens (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Patch CTF Estimation in cryoSPARC, fit local CTF to micrograph, including tilted, bent, deformed samples
Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio model was generated in cryoSPARC
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Resolution range 4-10 angstrom / Number images used: 28687
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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