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- EMDB-13725: Cryo electron sub-tomogram average of baseplate in Amoebophilus a... -

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Basic information

Entry
Database: EMDB / ID: EMD-13725
TitleCryo electron sub-tomogram average of baseplate in Amoebophilus asiaticus
Map data
Sample
  • Cell: The baseplate in Amoebophilus asiaticus
Function / homology
Function and homology information


acyltransferase activity / structural molecule activity
Similarity search - Function
Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Baseplate protein J-like / Baseplate J-like protein / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : ...Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Baseplate protein J-like / Baseplate J-like protein / 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 / LysM domain profile. / LysM domain
Similarity search - Domain/homology
Uncharacterized protein / Baseplate protein J-like domain-containing protein / Putative tail lysozyme / LysM domain-containing protein / Phospholipid/glycerol acyltransferase / Phage tail protein / Putative phage tail sheath protein FI
Similarity search - Component
Biological speciesCandidatus Amoebophilus asiaticus (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
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
  • Surface view with section colored by density value
  • Surface level: 0.38
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.38
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13725.png

Downloads & links

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Map

FileDownload / File: emd_13725.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.38 Å/pix.
x 96 pix.
= 516.48 Å		5.38 Å/pix.
x 96 pix.
= 516.48 Å		5.38 Å/pix.
x 96 pix.
= 516.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38 / Movie #1: 0.38
Minimum - Maximum-3.0325162 - 2.5545816
Average (Standard dev.)0.007818096 (±0.31259292)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 516.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.385.385.38
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z516.480516.480516.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-3.0332.5550.008

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Supplemental data

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Sample components

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Entire : The baseplate in Amoebophilus asiaticus

EntireName: The baseplate in Amoebophilus asiaticus
Components
  • Cell: The baseplate in Amoebophilus asiaticus

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Supramolecule #1: The baseplate in Amoebophilus asiaticus

SupramoleculeName: The baseplate in Amoebophilus asiaticus / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Candidatus Amoebophilus asiaticus (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 3.6 e/Å2
Details: 3.6 electrons for each tilt, while total ~150 electron for one tilt series (41 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 reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 366
ExtractionNumber tomograms: 68 / Number images used: 366
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: Dynamo

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