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- EMDB-31358: PVC-Empty baseplate -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-31358
TitlePVC-Empty baseplate
Map dataPVC-Empty baseplate
Sample
  • Complex: PVC-Empty baseplate
Biological speciesPhotorhabdus asymbiotica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWang X / Cheng J / Shen J / Liu L / Li N / Gao N / Jiang F / Jin Q
Funding support1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)
CitationJournal: Sci China Life Sci / Year: 2022
Title: Characterization of Photorhabdus Virulence Cassette as a causative agent in the emerging pathogen Photorhabdus asymbiotica.
Authors: Xia Wang / Jiaxuan Cheng / Jiawei Shen / Liguo Liu / Ningning Li / Ning Gao / Feng Jiang / Qi Jin /
Abstract: The extracellular contractile injection systems (eCISs) are encoded in the genomes of a large number of bacteria and archaea. We have previously characterized the overall structure of Photorhabdus ...The extracellular contractile injection systems (eCISs) are encoded in the genomes of a large number of bacteria and archaea. We have previously characterized the overall structure of Photorhabdus Virulence Cassette (PVC), a typical member of the eCIS family. PVC resembles the contractile tail of bacteriophages and exerts its action by the contraction of outer sheath and injection of inner tube plus central spike. Nevertheless, the biological function of PVC effectors and the mechanism of effector translocation are still lacking. By combining cryo-electron microscopy and functional experiments, here we show that the PVC effectors Pdp1 (a new family of widespread dNTP pyrophosphatase effector in eCIS) and Pnf (a deamidase effector) are loaded inside the inner tube lumen in a "Peas in the Pod" mode. Moreover, we observe that Pdp1 and Pnf can be directly injected into J774A.1 murine macrophage and kill the target cells by disrupting the dNTP pools and actin cytoskeleton formation, respectively. Our results provide direct evidence of how PVC cargoes are loaded and delivered directly into mammalian macrophages.
History
DepositionMay 25, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateMar 9, 2022-
Current statusMar 9, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31358.png

Downloads & links

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Map

FileDownload / File: emd_31358.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPVC-Empty baseplate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 433.92 Å		1.36 Å/pix.
x 320 pix.
= 433.92 Å		1.36 Å/pix.
x 320 pix.
= 433.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.356 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.2145557 - 0.34544566
Average (Standard dev.)0.0017175807 (±0.013166223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 433.91998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3561.3561.356
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z433.920433.920433.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ330330330
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2150.3450.002

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Supplemental data

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Sample components

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Entire : PVC-Empty baseplate

EntireName: PVC-Empty baseplate
Components
  • Complex: PVC-Empty baseplate

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Supramolecule #1: PVC-Empty baseplate

SupramoleculeName: PVC-Empty baseplate / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Photorhabdus asymbiotica (bacteria)
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6229
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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