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- EMDB-23791: Subtomogram average of Photosystem II 2D semicrystalline array on... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23791 | |||||||||
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Title | Subtomogram average of Photosystem II 2D semicrystalline array on thylakoid membranes isolated from Phaeodactylum tricornutum | |||||||||
![]() | Subtomogram average of Photosystem II 2D semicrystalline array on thylakoid membranes isolated from Phaeodactylum tricornutum | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 37.0 Å | |||||||||
![]() | Jiang J / Cheong KY / Falkowski PG / Dai W | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Integrating on-grid immunogold labeling and cryo-electron tomography to reveal photosystem II structure and spatial distribution in thylakoid membranes. Authors: Jennifer Jiang / Kuan Yu Cheong / Paul G Falkowski / Wei Dai / ![]() Abstract: A long-standing challenge in cell biology is elucidating the structure and spatial distribution of individual membrane-bound proteins, protein complexes and their interactions in their native ...A long-standing challenge in cell biology is elucidating the structure and spatial distribution of individual membrane-bound proteins, protein complexes and their interactions in their native environment. Here, we describe a workflow that combines on-grid immunogold labeling, followed by cryo-electron tomography (cryoET) imaging and structural analyses to identify and characterize the structure of photosystem II (PSII) complexes. Using an antibody specific to a core subunit of PSII, the D1 protein (uniquely found in the water splitting complex in all oxygenic photoautotrophs), we identified PSII complexes in biophysically active thylakoid membranes isolated from a model marine diatom Phaeodactylum tricornutum. Subsequent cryoET analyses of these protein complexes resolved two PSII structures: supercomplexes and dimeric cores. Our integrative approach establishes the structural signature of multimeric membrane protein complexes in their native environment and provides a pathway to elucidate their high-resolution structures. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.2 KB 10.2 KB | Display Display | ![]() |
Images | ![]() | 100.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 309.7 KB | Display | ![]() |
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Full document | ![]() | 309.2 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Subtomogram average of Photosystem II 2D semicrystalline array on thylakoid membranes isolated from Phaeodactylum tricornutum | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.454 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Photosystem II 2D semicrystalline array
Entire | Name: Photosystem II 2D semicrystalline array |
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Components |
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-Supramolecule #1: Photosystem II 2D semicrystalline array
Supramolecule | Name: Photosystem II 2D semicrystalline array / type: complex / ID: 1 / Parent: 0 Details: On thylakoid membranes isolated from Phaeodactylum tricornutum |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | 2D array |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 49000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 263 |
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Extraction | Number tomograms: 1 / Number images used: 263 |
CTF correction | Software - Name: EMAN2 |
Final angle assignment | Type: NOT APPLICABLE |