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- EMDB-13775: Subtomogram average of baseplate region of contractile injection ... -

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Basic information

Entry
Database: EMDB / ID: EMD-13775
TitleSubtomogram average of baseplate region of contractile injection systems in Anabaena PCC 7120 ghost cells in contracted state
Map dataSubtomogram average of baseplate region of contractile injection systems in Anabaena PCC 7120 ghost cells in contracted state
Sample
  • Complex: Baseplate region of contractile injection systems of Anabaena PCC 7120 ghost cells in contracted state
KeywordscryoET / cyanobacteria / contractile injection systems / CIS / CONTRACTILE PROTEIN
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 50.0 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: 26.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 26.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13775.png

Downloads & links

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Map

FileDownload / File: emd_13775.map.gz / Format: CCP4 / Size: 63.5 KB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationSubtomogram average of baseplate region of contractile injection systems in Anabaena PCC 7120 ghost cells in contracted state
Voxel sizeX=Y=Z: 17.2 Å
Density
Contour LevelBy AUTHOR: 26.800000000000001 / Movie #1: 26.8
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-2.3508437 (±33.103209999999997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions404040
Spacing404040
CellA=B=C: 688.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z17.217.217.2
M x/y/z404040
origin x/y/z0.0000.0000.000
length x/y/z688.000688.000688.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS404040
D min/max/mean-128.000127.000-2.351

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Supplemental data

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Sample components

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

EntireName: Baseplate region of contractile injection systems of Anabaena PCC 7120 ghost cells in contracted state
Components
  • Complex: Baseplate region of contractile injection systems of Anabaena PCC 7120 ghost cells in contracted state

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

SupramoleculeName: Baseplate region of contractile injection systems of Anabaena PCC 7120 ghost cells in contracted 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: 50.0 Å / Resolution method: OTHER / Number subtomograms used: 11
ExtractionNumber tomograms: 6 / Number images used: 11
Final angle assignmentType: NOT APPLICABLE

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