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Yorodumi- PDB-7b5h: Cryo-EM structure of the contractile injection system base plate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b5h | ||||||
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Title | Cryo-EM structure of the contractile injection system base plate from Anabaena PCC7120 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / contractile tail / injection system / macromolecular machine | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Eisenstein, F. / Weiss, G.L. / Pilhofer, M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7b5h.cif.gz | 7.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7b5h.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7b5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b5h_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7b5h_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7b5h_validation.xml.gz | 962.3 KB | Display | |
Data in CIF | 7b5h_validation.cif.gz | 1.5 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/7b5h ftp://data.pdbj.org/pub/pdb/validation_reports/b5/7b5h | HTTPS FTP |
-Related structure data
Related structure data | 12029MC 7b5iC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 10 types, 93 molecules AAABACBABBBCCACBCCDADBDCEAEBECFAFBFCADBDCDDDEDFDAEAFAGBEBFBG...
#1: Protein | Mass: 166114.344 Da / Num. of mol.: 18 / Fragment: crown protein Cis19 / 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: Q8YRX8 #2: Protein | Mass: 154377.031 Da / Num. of mol.: 6 / Fragment: baseplate protein Cis12 / 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: Q8YRX7 #3: Protein | Mass: 18335.021 Da / Num. of mol.: 18 / Fragment: tail fibre protein Cis13 / 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: Q8YRX6 #4: Protein | Mass: 139003.422 Da / Num. of mol.: 6 / Fragment: baseplate protein Cis11 / 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: Q8YRX5 #5: Protein | Mass: 63636.625 Da / Num. of mol.: 3 / Fragment: spike protein Cis8 / 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: Q8YRX2 #7: Protein | Mass: 16764.764 Da / Num. of mol.: 6 / Fragment: baseplate protein Cis9 / 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: Q8YRX4 #8: Protein | Mass: 27090.568 Da / Num. of mol.: 6 / Fragment: tube adapter protein Cis7 / 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: Q8YRX1 #9: Protein | Mass: 19204.932 Da / Num. of mol.: 6 / Fragment: tube adapter protein Cis5 / 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: Q8YRW9 #10: Protein | Mass: 16459.543 Da / Num. of mol.: 6 / Fragment: tube protein Cis1 / 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 #11: Protein | Mass: 53236.160 Da / Num. of mol.: 18 / Fragment: sheath protein Cis2 / 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 |
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-Protein/peptide , 1 types, 3 molecules ALCLEL
#6: Protein/peptide | Mass: 5226.893 Da / Num. of mol.: 3 / Fragment: spike plug protein Cis6 / 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: Q8YRX0 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Base plate and spike complex (C3) of the Anabaena PCC7120 contractile injection system Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated defocus min: 900 nm / Calibrated defocus max: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron 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 scans | Movie frames/image: 50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 228163 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36909 / Symmetry type: POINT |