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- EMDB-13722: Cryo electron tomogram of purified AlgoCIS wild-type. -

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Basic information

Entry
Database: EMDB / ID: EMD-13722
TitleCryo electron tomogram of purified AlgoCIS wild-type.
Map data
Sample
  • Complex: The purified extracellular contractile injection system (AlgoCIS) wild-type
Biological speciesAlgoriphagus machipongonensis (bacteria)
Methodelectron tomography / cryo EM
AuthorsXu J / Ericson C / Feldmueller M / Lien YW / Eisenstein F / Pilhofer M
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)679209 Switzerland
Swiss National Science Foundation31003A_179255 Switzerland
CitationJournal: Nat Microbiol / Year: 2022
Title: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis.
Authors: Jingwei Xu / Charles F Ericson / Yun-Wei Lien / Florentine U N Rutaganira / Fabian Eisenstein / Miki Feldmüller / Nicole King / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). ...Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a 'cap adaptor' located at the distal end, a 'plug' exposed to the tube lumen, and a 'cage' formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re-engineering CISs.
History
DepositionOct 11, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_13722.png

Downloads & links

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Map

FileDownload / File: emd_13722.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.74 Å/pix.
x 400 pix.
= 4296. Å		10.74 Å/pix.
x 1440 pix.
= 15465.6 Å		10.74 Å/pix.
x 1024 pix.
= 10997.76 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.74 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-418.0 - 261.0
Average (Standard dev.)2.2739258 (±6.436262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin209-208200
Dimensions14401024400
Spacing10241440400
CellA: 10997.76 Å / B: 15465.6 Å / C: 4296.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z10.7410.7410.74
M x/y/z10241440400
origin x/y/z0.0000.0000.000
length x/y/z10997.76015465.6004296.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS-208209200
NC/NR/NS10241440400
D min/max/mean-418.000261.0002.274

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Supplemental data

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Sample components

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Entire : The purified extracellular contractile injection system (AlgoCIS)...

EntireName: The purified extracellular contractile injection system (AlgoCIS) wild-type
Components
  • Complex: The purified extracellular contractile injection system (AlgoCIS) wild-type

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Supramolecule #1: The purified extracellular contractile injection system (AlgoCIS)...

SupramoleculeName: The purified extracellular contractile injection system (AlgoCIS) wild-type
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 2.1 e/Å2
Details: 2.1 electrons for each tilt, while total ~130 electron for one tilt series (61 tilts).
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 reconstructionSoftware - Name: IMOD / Number images used: 61

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