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- EMDB-51566: Cryo-EM structure of a contractile injection system in Streptomyc... -

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Basic information

Entry
Database: EMDB / ID: EMD-51566
TitleCryo-EM structure of a contractile injection system in Streptomyces coelicolor, the cap portion in extended state.
Map data
Sample
  • Complex: The cap module of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Pvc16 N-terminal domain-containing protein
KeywordsContractile injection system / STRUCTURAL PROTEIN
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Pvc16, N-terminal / Pvc16 N-terminal domain / 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 ...Pvc16, N-terminal / Pvc16 N-terminal domain / 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
Pvc16 N-terminal domain-containing protein / Phage tail sheath family protein / Phage tail protein
Similarity search - Component
Biological speciesStreptomyces coelicolor A3(2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCasu B / Sallmen JW / Hass PE / Afanasyev P / Xu J / Schlimpert S / Pilhofer M
Funding support Switzerland, European Union, United Kingdom, 4 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
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01097X/1 United Kingdom
CitationJournal: Elife / Year: 2025
Title: Function and firing of the contractile injection system requires the membrane protein CisA.
Authors: Bastien Casu / Joseph W Sallmen / Peter E Haas / Govind Chandra / Pavel Afanasyev / Jingwei Xu / Martin Pilhofer / Susan Schlimpert /
Abstract: Bacterial contractile injection systems (CIS) are phage tail-like macromolecular complexes that mediate cell-cell interactions by injecting effector proteins into target cells. CIS from (CIS) are ...Bacterial contractile injection systems (CIS) are phage tail-like macromolecular complexes that mediate cell-cell interactions by injecting effector proteins into target cells. CIS from (CIS) are localized in the cytoplasm. Under stress, they induce cell death and impact the life cycle. It remains unknown, however, whether CIS require accessory proteins to directly interact with the cytoplasmic membrane to function. Here, we characterize the putative membrane adaptor CisA, a conserved factor in CIS gene clusters across species. We show by cryo-electron tomography imaging and in vivo assays that CIS contraction and function depend on CisA. Using single-particle cryo-electron microscopy, we provide an atomic model of the extended CIS apparatus; however, CisA is not part of the complex. Instead, our findings show that CisA is a membrane protein with a cytoplasmic N-terminus predicted to interact with CIS components, thereby providing a possible mechanism for mediating CIS recruitment to the membrane and subsequent firing. Our work shows that CIS function in multicellular bacteria is distinct from type VI secretion systems and extracellular CIS, and possibly evolved due to the role CIS play in regulated cell death.
History
DepositionSep 18, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51566.png

Downloads & links

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Map

FileDownload / File: emd_51566.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 420 pix.
= 447.3 Å		1.07 Å/pix.
x 420 pix.
= 447.3 Å		1.07 Å/pix.
x 420 pix.
= 447.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.421
Minimum - Maximum-1.8494335 - 3.2251318
Average (Standard dev.)0.0024821006 (±0.119147025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 447.30002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51566_msk_1.map
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Half map: #2

Fileemd_51566_half_map_1.map
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Histogram

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Half map: #1

Fileemd_51566_half_map_2.map
Projections & Slices
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Sample components

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Entire : The cap module of a contractile injection system in Streptomyces ...

EntireName: The cap module of a contractile injection system in Streptomyces coelicolor
Components
  • Complex: The cap module of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Pvc16 N-terminal domain-containing protein

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Supramolecule #1: The cap module of a contractile injection system in Streptomyces ...

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

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Macromolecule #1: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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

UniProtKB: Phage tail protein

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Macromolecule #2: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / 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

UniProtKB: Phage tail sheath family protein

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Macromolecule #3: Pvc16 N-terminal domain-containing protein

MacromoleculeName: Pvc16 N-terminal domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 24.713115 KDa
SequenceString: MIHEVDEVLK ALLKGGALTD SGIDVAFEAP TRDWAARRNA PVVNAYLYDI REDVGRRHRG QVAVRDQDDI VVKRRQPPRW FRLSYLVTA WTKTPQDEHR LLSAVLATLL PREQLPPYEL PGALGAMNLP VPMTVAGVQT ESRSLAEIWS ALGGELKPSL D LVVTAPFP ...String:
MIHEVDEVLK ALLKGGALTD SGIDVAFEAP TRDWAARRNA PVVNAYLYDI REDVGRRHRG QVAVRDQDDI VVKRRQPPRW FRLSYLVTA WTKTPQDEHR LLSAVLATLL PREQLPPYEL PGALGAMNLP VPMTVAGVQT ESRSLAEIWS ALGGELKPSL D LVVTAPFP AYPEYDAGPP VTEGATVRIG GVEGDPPMSE GRSHRPHQVA AARAARKAVT DGRTKRQ

UniProtKB: Pvc16 N-terminal domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19218
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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