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- EMDB-16098: Cryo-EM structure of a contractile injection system in Streptomyc... -

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Basic information

Entry
Database: EMDB / ID: EMD-16098
TitleCryo-EM structure of a contractile injection system in Streptomyces coelicolor, the contracted sheath shell.
Map data
Sample
  • Complex: The sheath structure of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Phage tail sheath protein
Function / homologyPhage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / 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 / Phage tail sheath protein
Function and homology information
Biological speciesStreptomyces coelicolor A3(2) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsCasu B / Sallmen JW / Schlimpert S / Pilhofer M
Funding support Switzerland, European Union, United Kingdom, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179255 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_16098.png

Downloads & links

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Map

FileDownload / File: emd_16098.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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: 0.04
Minimum - Maximum-0.10362222 - 0.22200944
Average (Standard dev.)0.002663048 (±0.014798531)
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_16098_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_16098_half_map_2.map
Projections & Slices
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Sample components

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Entire : The sheath structure of a contractile injection system in Strepto...

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

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Supramolecule #1: The sheath structure of a contractile injection system in Strepto...

SupramoleculeName: The sheath structure 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 protein

MacromoleculeName: Phage tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 57.009609 KDa
SequenceString: MPSYLSPGVY VEEVASGSRP IEGVGTSVAA FVGLAPTGPL NEPTLVTNWT QYVAAFGDFT GGYYLAHSVY GFFNNGGSAA YVVRVGGSA EDAAADGSVN GAAAPAAVTG STAKALPAAE PKQLGTFAVT ATAAGQSGPL TVEVADPEGE GPAERFKLIV K DGDKPVET ...String:
MPSYLSPGVY VEEVASGSRP IEGVGTSVAA FVGLAPTGPL NEPTLVTNWT QYVAAFGDFT GGYYLAHSVY GFFNNGGSAA YVVRVGGSA EDAAADGSVN GAAAPAAVTG STAKALPAAE PKQLGTFAVT ATAAGQSGPL TVEVADPEGE GPAERFKLIV K DGDKPVET FDVSAKKGNR SYVVTQVKER SKLITVTEAA PSAQLVRPEN QSLTLPAPPS AAPAVPAGQA ESAHPGPAQY LG DSSDRTG FGGLEAIDEI SMVAVPDLMA AYQRGAIDLE AVKAVQLGLI AHCELMGDRV AIIDPPPNQN ARQIRVWRQE TAG YDSKYA ALYYPWIKSF DPATGQSRLV PPSGHVAGIW ARNDSERGVH KAPANEVVRG AVDLELQITR GEQDLLNPIG VNCI RSFPG RGIRVWGART LSSDPAWRYL NIRRYFNYLE ESILIGTQWV VFEPNDHNLW ARIRRNVSAF LVNEWRNGAL FGQSP DQAY YVKCDEETNP PESVDLGRVV CEIGIAPVKP AEFVIFRLAQ FSSGGGELDE

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

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Image processing

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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4854
Startup modelType of model: EMDB MAP
EMDB ID:

11747

Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8bky:
Cryo-EM structure of a contractile injection system in Streptomyces coelicolor, the contracted sheath shell.

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