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- PDB-7b5i: Cryo-EM structure of the contractile injection system cap complex... -

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Basic information

Entry
Database: PDB / ID: 7b5i
TitleCryo-EM structure of the contractile injection system cap complex from Anabaena PCC7120
Components
  • All3324 protein
  • All3325 protein
  • All3326 protein
  • All3327 protein
KeywordsPROTEIN TRANSPORT / contractile tail / injection system / macromolecular machine / contractile protein
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
All3327 protein / All3326 protein / All3325 protein / All3324 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsEisenstein, F. / Weiss, G.L. / Pilhofer, M.
CitationJournal: Nat Microbiol / Year: 2022
Title: Structure of a thylakoid-anchored contractile injection system in multicellular cyanobacteria.
Authors: Gregor L Weiss / Fabian Eisenstein / Ann-Katrin Kieninger / Jingwei Xu / Hannah A Minas / Milena Gerber / Miki Feldmüller / Iris Maldener / Karl Forchhammer / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 ...Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 secretion systems (T6SSs) are attached to the cytoplasmic membrane and function upon cell-cell contact. Here, we characterized a CIS in the multicellular cyanobacterium Anabaena, with features distinct from extracellular CISs and T6SSs. Cryo-electron tomography of focused ion beam-milled cells revealed that CISs were anchored in thylakoid membrane stacks, facing the cell periphery. Single particle cryo-electron microscopy showed that this unique in situ localization was mediated by extensions of tail fibre and baseplate components. On stress, cyanobacteria induced the formation of ghost cells, presenting thylakoid-anchored CISs to the environment. Functional assays suggest that these CISs may mediate ghost cell formation and/or interactions of ghost cells with other organisms. Collectively, these data provide a framework for understanding the evolutionary re-engineering of CISs and potential roles of these CISs in cyanobacterial programmed cell death.
History
DepositionDec 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / Item: _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 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure viewerMolecule:
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Assembly

Deposited unit
AA: All3327 protein
AB: All3326 protein
AC: All3325 protein
AD: All3324 protein
AE: All3324 protein
BA: All3327 protein
BB: All3326 protein
BC: All3325 protein
BD: All3324 protein
BE: All3324 protein
CA: All3327 protein
CB: All3326 protein
CC: All3325 protein
CD: All3324 protein
CE: All3324 protein
DA: All3327 protein
DB: All3326 protein
DC: All3325 protein
DD: All3324 protein
DE: All3324 protein
EA: All3327 protein
EB: All3326 protein
EC: All3325 protein
ED: All3324 protein
EE: All3324 protein
FA: All3327 protein
FB: All3326 protein
FC: All3325 protein
FD: All3324 protein
FE: All3324 protein


Theoretical massNumber of molelcules
Total (without water)920,63430
Polymers920,63430
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, in situ structures of the full assembly have been determined by cryo-electron tomography
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area152930 Å2
ΔGint-693 kcal/mol
Surface area345020 Å2
MethodPISA

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Components

#1: Protein
All3327 protein


Mass: 21935.064 Da / Num. of mol.: 6 / Fragment: cap protein Cis16A / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRW5
#2: Protein
All3326 protein


Mass: 45348.633 Da / Num. of mol.: 6 / Fragment: cap protein Cis16A / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRW6
#3: Protein
All3325 protein


Mass: 53236.160 Da / Num. of mol.: 6 / Fragment: cap protein Cis16A / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRW7
#4: Protein
All3324 protein


Mass: 16459.543 Da / Num. of mol.: 12 / Fragment: cap protein Cis16A / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRW8
Has protein modificationY

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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: Cap complex of the Anabaena PCC7120 contractile injection system
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 281 K

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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 / Calibrated defocus min: 900 nm / Calibrated defocus max: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 19000
Image scansMovie frames/image: 50

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2SerialEMimage acquisition
4GctfCTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 433028
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22598 / Symmetry type: POINT

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