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- EMDB-53139: Cryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-53139
TitleCryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in extended state
Map dataCryo-EM structure of the PlPVC cap in extended state
Sample
  • Complex: PlPVC cap (C6) in extended state
    • Protein or peptide: DUF4255 domain-containing protein
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein
KeywordsContractile injection system / VIRUS LIKE PARTICLE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.46 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_53139.png

Downloads & links

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Map

FileDownload / File: emd_53139.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the PlPVC cap in extended state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 560 pix.
= 672. Å		1.2 Å/pix.
x 560 pix.
= 672. Å		1.2 Å/pix.
x 560 pix.
= 672. 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: 0.35
Minimum - Maximum-0.57271016 - 1.4613732
Average (Standard dev.)-0.000006120524 (±0.045746196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 672.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of the PlPVC cap in extended state

Fileemd_53139_half_map_1.map
AnnotationCryo-EM structure of the PlPVC cap in extended 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 cap in extended state

Fileemd_53139_half_map_2.map
AnnotationCryo-EM structure of the PlPVC cap in extended 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 : PlPVC cap (C6) in extended state

EntireName: PlPVC cap (C6) in extended state
Components
  • Complex: PlPVC cap (C6) in extended state
    • Protein or peptide: DUF4255 domain-containing protein
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein

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Supramolecule #1: PlPVC cap (C6) in extended state

SupramoleculeName: PlPVC cap (C6) in extended state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus luminescens (bacteria)

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Macromolecule #1: DUF4255 domain-containing protein

MacromoleculeName: DUF4255 domain-containing protein / type: protein_or_peptide / ID: 1 / Details: Pvc16 - cap protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 33.299473 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTIIIASDNA IIEINQALNT ILSQYLNITG QNIDIRFDLP EINSIQSEPT VSVFLYEIHE DLQLRSAESR RYNPSTNTLL PGWVNINCN YLITYWDASK PSSDSSSPDS QPNNQAAQVM TRILNALINN RQLTGLPGAY TRIIPQQENL NSLGNFWQAL G NRPRLSLL ...String:
MTIIIASDNA IIEINQALNT ILSQYLNITG QNIDIRFDLP EINSIQSEPT VSVFLYEIHE DLQLRSAESR RYNPSTNTLL PGWVNINCN YLITYWDASK PSSDSSSPDS QPNNQAAQVM TRILNALINN RQLTGLPGAY TRIIPQQENL NSLGNFWQAL G NRPRLSLL YSITVPMKLK NIEDNVIPVS KISASVDQKP NLDNSQINQA LIDKLCVELG GTEDVRLALA KVNLTTKPDT EN NQNQENE SVIVEVSGIT SVTYLPQIKD TLTKWKSSQE AIVKINGVSI VVSKENADKL IGI

UniProtKB: DUF4255 domain-containing protein

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Macromolecule #2: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 2 / Details: Pvc1 - tube protein / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 16.574574 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAITPEQIAV EYPIPTYRFV VSVGDEQIPF NNVSGLDVHY DVIEYKDGIG NYYKMPGQRQ SINITLRKGV FPGDTKLFDW INSIQLNQV EKKDIAISLT NEAGTEILMT WNVANAFPTS FTSPSFDATS NEIAVQEIAL TADRVTIQAA

UniProtKB: Phage tail protein

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Macromolecule #3: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 3 / Details: Pvc2 - sheath protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 39.009828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTITTYPGV YIEEDASLSL SVSSSATAVP VFAVAGDNPL ISGKPYIRIS NWLEYLTLKN EQFDPANTLD ISLRAYFING GGYCYLVQT TDLEKQVPKL DDVTLLVAAG ENITTAVSTL CKPGKGLFAI FDGPTTELKS DGTSNSDYDP NPFAAVYYPW L TADWTTTI ...String:
MTTITTYPGV YIEEDASLSL SVSSSATAVP VFAVAGDNPL ISGKPYIRIS NWLEYLTLKN EQFDPANTLD ISLRAYFING GGYCYLVQT TDLEKQVPKL DDVTLLVAAG ENITTAVSTL CKPGKGLFAI FDGPTTELKS DGTSNSDYDP NPFAAVYYPW L TADWTTTI DIPPSAAIAG VYCSVDSTRG VWKAPANVPI QGGLQPKYPV TDDLQAQYNQ GKALNMIRTF PKSGTLVWGA RT LEDNDNW RYIPVRRLFN SAERDIKNAM SFAVFEPNSQ PTWERVRSAV NNYLYSLWQQ GGLAGNKPDD AYFVQIGKDI TMT DDDIKQ GKMIIKIGMA AVRPAEFIIL QFTQNTAQ

UniProtKB: Phage tail sheath family protein

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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: 7.4
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: 41.0 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: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57353
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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