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Yorodumi- EMDB-0540: Averaged structure of Photosystem II 2D crystalline array on thyl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0540 | ||||||||||||
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Title | Averaged structure of Photosystem II 2D crystalline array on thylakoid membrane from diatom | ||||||||||||
Map data | Averaged structure of PSII array on thylakoid membrane from diatom | ||||||||||||
Sample |
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Biological species | Phaeodactylum tricornutum (Diatom) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 10.4 Å | ||||||||||||
Authors | Chen M / Kuang X / Levitan O / Falkowski P / Dai W | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Structural and functional analyses of photosystem II in the marine diatom . Authors: Orly Levitan / Muyuan Chen / Xuyuan Kuang / Kuan Yu Cheong / Jennifer Jiang / Melissa Banal / Nikhita Nambiar / Maxim Y Gorbunov / Steven J Ludtke / Paul G Falkowski / Wei Dai / Abstract: A descendant of the red algal lineage, diatoms are unicellular eukaryotic algae characterized by thylakoid membranes that lack the spatial differentiation of stroma and grana stacks found in green ...A descendant of the red algal lineage, diatoms are unicellular eukaryotic algae characterized by thylakoid membranes that lack the spatial differentiation of stroma and grana stacks found in green algae and higher plants. While the photophysiology of diatoms has been studied extensively, very little is known about the spatial organization of the multimeric photosynthetic protein complexes within their thylakoid membranes. Here, using cryo-electron tomography, proteomics, and biophysical analyses, we elucidate the macromolecular composition, architecture, and spatial distribution of photosystem II complexes in diatom thylakoid membranes. Structural analyses reveal 2 distinct photosystem II populations: loose clusters of complexes associated with antenna proteins and compact 2D crystalline arrays of dimeric cores. Biophysical measurements reveal only 1 photosystem II functional absorption cross section, suggesting that only the former population is photosynthetically active. The tomographic data indicate that the arrays of photosystem II cores are physically separated from those associated with antenna proteins. We hypothesize that the islands of photosystem cores are repair stations, where photodamaged proteins can be replaced. Our results strongly imply convergent evolution between the red and the green photosynthetic lineages toward spatial segregation of dynamic, functional microdomains of photosystem II supercomplexes. | ||||||||||||
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_0540.map.gz | 1.3 MB | EMDB map data format | |
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Header (meta data) | emd-0540-v30.xml emd-0540.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0540_fsc.xml | 4.7 KB | Display | FSC data file |
Images | emd_0540.png | 180.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0540 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0540 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0540.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Averaged structure of PSII array on thylakoid membrane from diatom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.65 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 : Thylakoid membrane purified from diatom
Entire | Name: Thylakoid membrane purified from diatom |
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Components |
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-Supramolecule #1: Thylakoid membrane purified from diatom
Supramolecule | Name: Thylakoid membrane purified from diatom / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Phaeodactylum tricornutum (Diatom) / Organelle: Thylakoid membrane |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: LEICA EM GP |
Details | Thylakoid membrane purified from diatom |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |