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

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Basic information

Entry
Database: PDB / ID: 7adz
TitleCryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the cap portion in extended state.
Components
  • Phage tail protein
  • Putative phage tail sheath protein FI
  • cap adaptor protein (Algo2)
  • cap protein (Algo1)
KeywordsSTRUCTURAL PROTEIN / extracellular contractile injection system
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Pvc16, N-terminal / Pvc16 N-terminal domain / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Phage tail protein / Putative phage tail sheath protein FI / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesAlgoriphagus machipongonensis (bacteria)
MethodELECTRON MICROSCOPY / single particle 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

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
0A: cap protein (Algo1)
0B: cap protein (Algo1)
0C: cap protein (Algo1)
0D: cap protein (Algo1)
0E: cap protein (Algo1)
0F: cap protein (Algo1)
1A: cap adaptor protein (Algo2)
1B: cap adaptor protein (Algo2)
1C: cap adaptor protein (Algo2)
1D: cap adaptor protein (Algo2)
1E: cap adaptor protein (Algo2)
1F: cap adaptor protein (Algo2)
1a: Phage tail protein
1b: Phage tail protein
1c: Phage tail protein
1d: Phage tail protein
1e: Phage tail protein
1f: Phage tail protein
2A: Putative phage tail sheath protein FI
2B: Putative phage tail sheath protein FI
2C: Putative phage tail sheath protein FI
2D: Putative phage tail sheath protein FI
2E: Putative phage tail sheath protein FI
2F: Putative phage tail sheath protein FI
2a: Phage tail protein
2b: Phage tail protein
2c: Phage tail protein
2d: Phage tail protein
2e: Phage tail protein
2f: Phage tail protein


Theoretical massNumber of molelcules
Total (without water)990,80630
Polymers990,80630
Non-polymers00
Water0
1


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

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Components

#1: Protein
cap protein (Algo1) / cap protein (Algo1)


Mass: 22981.086 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: cap protein (Algo1) / Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTC4
#2: Protein
cap adaptor protein (Algo2) / cap adaptor protein (Algo2)


Mass: 33083.371 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: cap adaptor protein (Algo2) / Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTC3
#3: Protein
Phage tail protein


Mass: 16375.458 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTC1
#4: Protein
Putative phage tail sheath protein FI


Mass: 76319.039 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: the residues (288-320aa) are not built up in the model and the residues (430-446aa) are assigned as poly-alanine due to the poor density map.
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: single particle reconstruction

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Sample preparation

ComponentName: The cap portion 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
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
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 FIELDBright-field microscopy
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
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65059 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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