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- PDB-7aek: Cryo-EM structure of an extracellular contractile injection syste... -

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Basic information

Entry
Database: PDB / ID: 7aek
TitleCryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the contracted sheath shell.
ComponentsPutative phage tail sheath protein FI
KeywordsSTRUCTURAL PROTEIN / extracellular contractile injection system
Function / homology: / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Putative phage tail sheath protein FI
Function and homology information
Biological speciesAlgoriphagus machipongonensis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsXu, J. / Ericson, C. / Feldmueller, M. / Lien, Y.W. / Pilhofer, M.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
European Research Council (ERC) Switzerland
Swiss National Science Foundation Switzerland
Other private Switzerland
CitationJournal: Nat Microbiol / Year: 2022
Title: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis.
Authors: Jingwei Xu / Charles F Ericson / Yun-Wei Lien / Florentine U N Rutaganira / Fabian Eisenstein / Miki Feldmüller / Nicole King / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). ...Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a 'cap adaptor' located at the distal end, a 'plug' exposed to the tube lumen, and a 'cage' formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re-engineering CISs.
History
DepositionSep 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Assembly

Deposited unit
3A: Putative phage tail sheath protein FI
3B: Putative phage tail sheath protein FI
3C: Putative phage tail sheath protein FI
3D: Putative phage tail sheath protein FI
3E: Putative phage tail sheath protein FI
3F: Putative phage tail sheath protein FI
4A: Putative phage tail sheath protein FI
4B: Putative phage tail sheath protein FI
4C: Putative phage tail sheath protein FI
4D: Putative phage tail sheath protein FI
4E: Putative phage tail sheath protein FI
4F: Putative phage tail sheath protein FI
5A: Putative phage tail sheath protein FI
5B: Putative phage tail sheath protein FI
5C: Putative phage tail sheath protein FI
5D: Putative phage tail sheath protein FI
5E: Putative phage tail sheath protein FI
5F: Putative phage tail sheath protein FI


Theoretical massNumber of molelcules
Total (without water)1,373,74318
Polymers1,373,74318
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Putative phage tail sheath protein FI


Mass: 76319.039 Da / Num. of mol.: 18 / Source method: isolated from a natural source
Details: the residues 288-320aa are not built up in the model due to the poor map density, with residues 430-446aa assigned by poly-alanine chain.
Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTC2

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: The contracted sheath shell of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis.
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Algoriphagus machipongonensis (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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 32.2 ° / Axial rise/subunit: 18.04 Å / Axial symmetry: C6
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92922 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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