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- EMDB-16101: Cryo-EM structure of a contractile injection system in Streptomyc... -

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Basic information

Entry
Database: EMDB / ID: EMD-16101
TitleCryo-EM structure of a contractile injection system in Streptomyces coelicolor, the sheath-tube module in extended state.
Map data
Sample
  • Complex: The sheath-tube module of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Phage tail protein
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Phage tail sheath family protein / Uncharacterized protein
Similarity search - Component
Biological speciesStreptomyces coelicolor A3(2) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsCasu B / Sallmen JW / Schlimpert S / Pilhofer M
Funding support Switzerland, European Union, United Kingdom, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation679209 Switzerland
European Research Council (ERC)679209European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T015349/1 United Kingdom
CitationJournal: Nat Microbiol / Year: 2023
Title: Cytoplasmic contractile injection systems mediate cell death in Streptomyces.
Authors: Bastien Casu / Joseph W Sallmen / Susan Schlimpert / Martin Pilhofer /
Abstract: Contractile injection systems (CIS) are bacteriophage tail-like structures that mediate bacterial cell-cell interactions. While CIS are highly abundant across diverse bacterial phyla, representative ...Contractile injection systems (CIS) are bacteriophage tail-like structures that mediate bacterial cell-cell interactions. While CIS are highly abundant across diverse bacterial phyla, representative gene clusters in Gram-positive organisms remain poorly studied. Here we characterize a CIS in the Gram-positive multicellular model organism Streptomyces coelicolor and show that, in contrast to most other CIS, S. coelicolor CIS (CIS) mediate cell death in response to stress and impact cellular development. CIS are expressed in the cytoplasm of vegetative hyphae and are not released into the medium. Our cryo-electron microscopy structure enabled the engineering of non-contractile and fluorescently tagged CIS assemblies. Cryo-electron tomography showed that CIS contraction is linked to reduced cellular integrity. Fluorescence light microscopy furthermore revealed that functional CIS mediate cell death upon encountering different types of stress. The absence of functional CIS had an impact on hyphal differentiation and secondary metabolite production. Finally, we identified three putative effector proteins, which when absent, phenocopied other CIS mutants. Our results provide new functional insights into CIS in Gram-positive organisms and a framework for studying novel intracellular roles, including regulated cell death and life-cycle progression in multicellular bacteria.
History
DepositionNov 9, 2022-
Header (metadata) releaseMar 15, 2023-
Map releaseMar 15, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16101.png

Downloads & links

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Map

FileDownload / File: emd_16101.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 320 pix.
= 448. Å		1.4 Å/pix.
x 320 pix.
= 448. Å		1.4 Å/pix.
x 320 pix.
= 448. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09253999 - 0.18338275
Average (Standard dev.)0.00134328 (±0.009772018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 448.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16101_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16101_half_map_2.map
Projections & Slices
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Sample components

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Entire : The sheath-tube module of a contractile injection system in Strep...

EntireName: The sheath-tube module of a contractile injection system in Streptomyces coelicolor
Components
  • Complex: The sheath-tube module of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Phage tail protein

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Supramolecule #1: The sheath-tube module of a contractile injection system in Strep...

SupramoleculeName: The sheath-tube module of a contractile injection system in Streptomyces coelicolor
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)

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Macromolecule #1: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 57.465113 KDa
SequenceString: MPSYLSPGVY VEEVASGSRP IEGVGIEGVG TSVAAFVGLA PTGPLNEPTL VTNWTQYVAA FGDFTGGYYL AHSVYGFFNN GGSAAYVVR VGGSAEDAAA DGSVNGAAAP AAVTGSTAKA LPAAEPKQLG TFAVTATAAG QSGPLTVEVA DPEGEGPAER F KLIVKDGD ...String:
MPSYLSPGVY VEEVASGSRP IEGVGIEGVG TSVAAFVGLA PTGPLNEPTL VTNWTQYVAA FGDFTGGYYL AHSVYGFFNN GGSAAYVVR VGGSAEDAAA DGSVNGAAAP AAVTGSTAKA LPAAEPKQLG TFAVTATAAG QSGPLTVEVA DPEGEGPAER F KLIVKDGD KPVETFDVSA KKGNRSYVVT QVKERSKLIT VTEAAPSAQL VRPENQSLTL PAPPSAAPAV PAGQAESAHP GP AQYLGDS SDRTGFGGLE AIDEISMVAV PDLMAAYQRG AIDLEAVKAV QLGLIAHCEL MGDRVAIIDP PPNQNARQIR VWR QETAGY DSKYAALYYP WIKSFDPATG QSRLVPPSGH VAGIWARNDS ERGVHKAPAN EVVRGAVDLE LQITRGEQDL LNPI GVNCI RSFPGRGIRV WGARTLSSDP AWRYLNIRRY FNYLEESILI GTQWVVFEPN DHNLWARIRR NVSAFLVNEW RNGAL FGQS PDQAYYVKCD EETNPPESVD LGRVVCEIGI APVKPAEFVI FRLAQFSSGG GELDE

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Macromolecule #2: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 16.493668 KDa
SequenceString:
MSLPKPEDVL VAPNFGIQID GVMVEYLNSV SNLQIEQDVI RYQQNQGTTG RNNVTLMPGV AKDGSVQVER GMSQSSVFTQ WINDSMAGR MATARKNATI IVMDYEDNPV KRWNLRNAWC SKVVAGTLKA GDTNALTETI TIVFEELVVE

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

11735

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 38.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 23.10 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18822

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