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

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Basic information

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: Marin-Arraiza L / Roa-Eguiara A / Pape T / Sofos N / Hendriks IA / Lund Nielsen M / Steiner-Rebrova EM / Taylor NMI
History
DepositionMar 14, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 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

Projections

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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