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Yorodumi- EMDB-4601: In situ defocus subtomogram average of phycobilisome array from S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4601 | |||||||||
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Title | In situ defocus subtomogram average of phycobilisome array from Synechocystis sp. PCC 6803 | |||||||||
Map data | In situ defocus subtomogram average of phycobilisome array from Synechocystis sp. PCC 6803 | |||||||||
Sample |
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Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 23.6 Å | |||||||||
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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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4601.map.gz | 58 MB | EMDB map data format | |
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Header (meta data) | emd-4601-v30.xml emd-4601.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_4601.png | 256.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4601 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4601 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4601.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | In situ defocus subtomogram average of phycobilisome array from Synechocystis sp. PCC 6803 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.42 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 : In situ defocus subtomogram average of phycobilisome array from S...
Entire | Name: In situ defocus subtomogram average of phycobilisome array from Synechocystis |
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Components |
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-Supramolecule #1: In situ defocus subtomogram average of phycobilisome array from S...
Supramolecule | Name: In situ defocus subtomogram average of phycobilisome array from Synechocystis type: complex / ID: 1 / Parent: 0 Details: Each unit of the array has a molecular weight of ~6 MDa. |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) / Location in cell: Cytosol |
Molecular weight | Theoretical: 30 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.006 µm / Nominal defocus min: 0.004 µm / Nominal magnification: 42000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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. |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 20 / Number images used: 3850 / Software - Name: PyTom (ver. 0.97) Details: Template matching followed by oversampling of splines along arrays. Duplicate points were removed following the alignment process. |
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CTF correction | Software - Name: IMOD (ver. 4.9) |
Final angle assignment | Type: OTHER / Details: Template matching with PyTom |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 23.6 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Averaging was performed with STOPGAP 0.3.1 / Number subtomograms used: 1710 |