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Yorodumi- EMDB-12029: Cryo-EM structure of the contractile injection system base plate ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12029 | |||||||||
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Title | Cryo-EM structure of the contractile injection system base plate from Anabaena PCC7120 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information | |||||||||
Biological species | Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Eisenstein F / Weiss GL / 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12029.map.gz | 401.7 MB | EMDB map data format | |
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Header (meta data) | emd-12029-v30.xml emd-12029.xml | 31.1 KB 31.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12029_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_12029.png | 202.9 KB | ||
Others | emd_12029_half_map_1.map.gz emd_12029_half_map_2.map.gz | 409.4 MB 410.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12029 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12029 | HTTPS FTP |
-Validation report
Summary document | emd_12029_validation.pdf.gz | 532.7 KB | Display | EMDB validaton report |
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Full document | emd_12029_full_validation.pdf.gz | 532.3 KB | Display | |
Data in XML | emd_12029_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | emd_12029_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12029 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12029 | HTTPS FTP |
-Related structure data
Related structure data | 7b5hMC 7b5iC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12029.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_12029_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12029_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Base plate and spike complex (C3) of the Anabaena PCC7120 contrac...
+Supramolecule #1: Base plate and spike complex (C3) of the Anabaena PCC7120 contrac...
+Macromolecule #1: All3314 protein
+Macromolecule #2: All3315 protein
+Macromolecule #3: All3316 protein
+Macromolecule #4: All3317 protein
+Macromolecule #5: All3320 protein
+Macromolecule #6: Asl3322 protein
+Macromolecule #7: All3318 protein
+Macromolecule #8: All3321 protein
+Macromolecule #9: All3323 protein
+Macromolecule #10: All3324 protein
+Macromolecule #11: All3325 protein
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 4 / Number real images: 19000 / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |