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- EMDB-13773: Subtomogram average of baseplate region of contractile injection ... -

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Basic information

Entry
Database: EMDB / ID: EMD-13773
TitleSubtomogram average of baseplate region of contractile injection systems in Anabaena PCC 7120 in extended state
Map dataSubtomogram average of baseplate region of contractile injection systems in Anabaena PCC 7120 in extended state
Sample
  • Complex: Baseplate region of contractile injection system of Anabaena PCC 7120 in extended state
KeywordscryoET / cyanobacteria / contractile injection systems / CIS / CONTRACTILE PROTEIN
Function / homology
Function and homology information


structural molecule activity / membrane
Similarity search - Function
Protein of unknown function DUF5908 / Family of unknown function (DUF5908) / YegP-like superfamily / 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 / Type VI secretion system, RhsGE-associated Vgr protein ...Protein of unknown function DUF5908 / Family of unknown function (DUF5908) / YegP-like superfamily / 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 / Type VI secretion system, RhsGE-associated Vgr protein / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
All3325 protein / All3324 protein / All3323 protein / Asl3322 protein / All3321 protein / All3320 protein / All3318 protein / All3317 protein / All3316 protein / All3315 protein / All3314 protein
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 29.1 Å
AuthorsWeiss GL / Eisenstein F / Pilhofer M
Funding support Japan, 6 items
OrganizationGrant numberCountry
European Research Council (ERC)679209 Japan
Swiss National Science Foundation31003A_179255 Japan
Boehringer Ingelheim Fonds (BIF) Japan
German Research Foundation (DFG)SFB766 Japan
German Research Foundation (DFG)GRK1708 Japan
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Microbiol / Year: 2022
Title: Structure of a thylakoid-anchored contractile injection system in multicellular cyanobacteria.
Authors: Gregor L Weiss / Fabian Eisenstein / Ann-Katrin Kieninger / Jingwei Xu / Hannah A Minas / Milena Gerber / Miki Feldmüller / Iris Maldener / Karl Forchhammer / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 ...Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 secretion systems (T6SSs) are attached to the cytoplasmic membrane and function upon cell-cell contact. Here, we characterized a CIS in the multicellular cyanobacterium Anabaena, with features distinct from extracellular CISs and T6SSs. Cryo-electron tomography of focused ion beam-milled cells revealed that CISs were anchored in thylakoid membrane stacks, facing the cell periphery. Single particle cryo-electron microscopy showed that this unique in situ localization was mediated by extensions of tail fibre and baseplate components. On stress, cyanobacteria induced the formation of ghost cells, presenting thylakoid-anchored CISs to the environment. Functional assays suggest that these CISs may mediate ghost cell formation and/or interactions of ghost cells with other organisms. Collectively, these data provide a framework for understanding the evolutionary re-engineering of CISs and potential roles of these CISs in cyanobacterial programmed cell death.
History
DepositionOct 21, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13773.png

Downloads & links

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Map

FileDownload / File: emd_13773.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of baseplate region of contractile injection systems in Anabaena PCC 7120 in extended state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.38 Å/pix.
x 160 pix.
= 540.8 Å		3.38 Å/pix.
x 160 pix.
= 540.8 Å		3.38 Å/pix.
x 160 pix.
= 540.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-1.766421 - 2.0350213
Average (Standard dev.)-0.052573875 (±0.33470133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 540.80005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.383.383.38
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z540.800540.800540.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-1.7662.035-0.053

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Supplemental data

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Half map: half map even, inverted

Fileemd_13773_half_map_1.map
Annotationhalf map even, inverted
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map odd, inverted

Fileemd_13773_half_map_2.map
Annotationhalf map odd, inverted
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Baseplate region of contractile injection system of Anabaena PCC ...

EntireName: Baseplate region of contractile injection system of Anabaena PCC 7120 in extended state
Components
  • Complex: Baseplate region of contractile injection system of Anabaena PCC 7120 in extended state

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Supramolecule #1: Baseplate region of contractile injection system of Anabaena PCC ...

SupramoleculeName: Baseplate region of contractile injection system of Anabaena PCC 7120 in extended state
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.3 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 reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 29.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 170
ExtractionNumber tomograms: 99 / Number images used: 204
Final angle assignmentType: NOT APPLICABLE

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