+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4604 | |||||||||
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Title | Defocus in situ tomogram of a Synechocystis cell | |||||||||
Map data | Defocus in situ tomogram of a Synechocystis cell | |||||||||
Sample |
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Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Rast A / Wan W / Pfeffer S / Engel BD | |||||||||
Citation | Journal: Nat Plants / Year: 2019 Title: Biogenic regions of cyanobacterial thylakoids form contact sites with the plasma membrane. Authors: Anna Rast / Miroslava Schaffer / Sahradha Albert / William Wan / Stefan Pfeffer / Florian Beck / Jürgen M Plitzko / Jörg Nickelsen / Benjamin D Engel / Abstract: Little is known about how the photosynthetic machinery is arranged in time and space during the biogenesis of thylakoid membranes. Using in situ cryo-electron tomography to image the three- ...Little is known about how the photosynthetic machinery is arranged in time and space during the biogenesis of thylakoid membranes. Using in situ cryo-electron tomography to image the three-dimensional architecture of the cyanobacterium Synechocystis, we observed that the tips of multiple thylakoids merge to form a substructure called the 'convergence membrane'. This high-curvature membrane comes into close contact with the plasma membrane at discrete sites. We generated subtomogram averages of 70S ribosomes and array-forming phycobilisomes, then mapped these structures onto the native membrane architecture as markers for protein synthesis and photosynthesis, respectively. This molecular localization identified two distinct biogenic regions in the thylakoid network: thylakoids facing the cytosolic interior of the cell that were associated with both marker complexes, and convergence membranes that were decorated by ribosomes but not phycobilisomes. We propose that the convergence membranes perform a specialized biogenic function, coupling the synthesis of thylakoid proteins with the integration of cofactors from the plasma membrane and the periplasmic space. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4604.map.gz | 348.5 MB | EMDB map data format | |
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Header (meta data) | emd-4604-v30.xml emd-4604.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_4604.png | 163.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4604 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4604 | HTTPS FTP |
-Validation report
Summary document | emd_4604_validation.pdf.gz | 212.7 KB | Display | EMDB validaton report |
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Full document | emd_4604_full_validation.pdf.gz | 211.9 KB | Display | |
Data in XML | emd_4604_validation.xml.gz | 4.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4604 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4604 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4604.map.gz / Format: CCP4 / Size: 762.2 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Defocus in situ tomogram of a Synechocystis cell | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 13.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Defocus in situ tomogram of a Synechocystis cell
Entire | Name: Defocus in situ tomogram of a Synechocystis cell |
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Components |
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-Supramolecule #1: Defocus in situ tomogram of a Synechocystis cell
Supramolecule | Name: Defocus in situ tomogram of a Synechocystis cell / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time: 10 sec Blot force: 10. |
Details | Vitrious Synechocystis cell milled with a Ga2+ focused ion beam. |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.03 nA / Focused ion beam - Duration: 3600 sec. / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 2000 nm / Focused ion beam - Final thickness: 150 nm Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Quanta FIB. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average exposure time: 1.5 sec. / Average electron dose: 1.5 e/Å2 Details: Images were collected in movie-mode at 12 frames per second. Higher tilts had longer exposures. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.005 µm / Nominal defocus min: 0.005 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.9) / Number images used: 60 |
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