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- PDB-9gtp: Cryo-EM structure of a contractile injection system in Streptomyc... -

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Basic information

Entry
Database: PDB / ID: 9gtp
TitleCryo-EM structure of a contractile injection system in Streptomyces coelicolor, the baseplate complex in extended state applied 6-fold symmetry.
Components
  • (Phage tail protein) x 2
  • Baseplate protein J-like domain-containing protein
  • IraD/Gp25-like domain-containing protein
  • LysM domain-containing protein
  • Phage tail sheath family protein
  • Secreted protein
KeywordsSTRUCTURAL PROTEIN / Contractile injection system
Function / homology
Function and homology information


lytic endotransglycosylase activity / peptidoglycan metabolic process / structural molecule activity
Similarity search - Function
Uncharacterised protein family, phage tail-like / Conserved hypothetical protein CHP02243 / Tail protein I / Phage tail protein (Tail_P2_I) / : / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Phage tail sheath protein, beta-sandwich domain / Baseplate wedge protein gp25 ...Uncharacterised protein family, phage tail-like / Conserved hypothetical protein CHP02243 / Tail protein I / Phage tail protein (Tail_P2_I) / : / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Phage tail sheath protein, beta-sandwich domain / Baseplate wedge protein gp25 / Phage tail sheath protein beta-sandwich domain / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Baseplate protein J-like / Baseplate J-like protein barrel 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 / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
Phage tail sheath family protein / Phage tail protein / Phage tail protein / LysM domain-containing protein / IraD/Gp25-like domain-containing protein / Baseplate protein J-like domain-containing protein / Secreted protein
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCasu, B. / Sallmen, J.W. / Haas, P.E. / Afanasyev, P. / Xu, J. / Schlimpert, S. / Pilhofer, M.
Funding support Switzerland, European Union, United Kingdom, 4items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
o: Phage tail protein
1h: Phage tail sheath family protein
1K: Baseplate protein J-like domain-containing protein
P: LysM domain-containing protein
2K: Baseplate protein J-like domain-containing protein
E: Secreted protein
V: IraD/Gp25-like domain-containing protein
a: Phage tail protein
2i: Phage tail sheath family protein
3i: Phage tail sheath family protein
p: Phage tail protein
1i: Phage tail sheath family protein
1L: Baseplate protein J-like domain-containing protein
Q: LysM domain-containing protein
2L: Baseplate protein J-like domain-containing protein
F: Secreted protein
W: IraD/Gp25-like domain-containing protein
b: Phage tail protein
2j: Phage tail sheath family protein
3j: Phage tail sheath family protein
k: Phage tail protein
1j: Phage tail sheath family protein
1G: Baseplate protein J-like domain-containing protein
R: LysM domain-containing protein
2G: Baseplate protein J-like domain-containing protein
A: Secreted protein
X: IraD/Gp25-like domain-containing protein
c: Phage tail protein
2e: Phage tail sheath family protein
3e: Phage tail sheath family protein
l: Phage tail protein
1e: Phage tail sheath family protein
1H: Baseplate protein J-like domain-containing protein
M: LysM domain-containing protein
2H: Baseplate protein J-like domain-containing protein
B: Secreted protein
S: IraD/Gp25-like domain-containing protein
d: Phage tail protein
2f: Phage tail sheath family protein
3f: Phage tail sheath family protein
m: Phage tail protein
1f: Phage tail sheath family protein
1l: Baseplate protein J-like domain-containing protein
N: LysM domain-containing protein
2l: Baseplate protein J-like domain-containing protein
C: Secreted protein
T: IraD/Gp25-like domain-containing protein
e: Phage tail protein
2g: Phage tail sheath family protein
3g: Phage tail sheath family protein
n: Phage tail protein
1g: Phage tail sheath family protein
1J: Baseplate protein J-like domain-containing protein
O: LysM domain-containing protein
2J: Baseplate protein J-like domain-containing protein
D: Secreted protein
U: IraD/Gp25-like domain-containing protein
f: Phage tail protein
2h: Phage tail sheath family protein
3h: Phage tail sheath family protein


Theoretical massNumber of molelcules
Total (without water)2,442,62460
Polymers2,442,62460
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 7 types, 60 molecules opklmn1h2i3i1i2j3j1j2e3e1e2f3f1f2g3g1g2h3h1K2K1L2L1G2G...

#1: Protein
Phage tail protein


Mass: 16493.668 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9L0N9
#2: Protein
Phage tail sheath family protein


Mass: 57009.609 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9L0N8
#3: Protein
Baseplate protein J-like domain-containing protein


Mass: 70889.352 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9L0P7
#4: Protein
LysM domain-containing protein


Mass: 25716.328 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9L0P4
#5: Protein
Secreted protein


Mass: 20282.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9L0P8
#6: Protein
IraD/Gp25-like domain-containing protein


Mass: 16609.537 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9L0P6
#7: Protein
Phage tail protein


Mass: 15194.927 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9L0P3

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The baseplate module applied 6-fold symmetry of a contractile injection system in Streptomyces coelicolor
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22980 / Symmetry type: POINT

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