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Yorodumi- EMDB-26569: Cryo-electron tomogram of non-treated onion cell wall from scale ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26569 | ||||||||||||
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Title | Cryo-electron tomogram of non-treated onion cell wall from scale #8 (related to Figure 3 of primary citation) | ||||||||||||
Map data | Cryo-electron tomogram of non-treated onion cell wall from scale #8 (related toFigure 3 of primary citation) | ||||||||||||
Sample |
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Biological species | Allium cepa (onion) | ||||||||||||
Method | electron tomography / cryo EM | ||||||||||||
Authors | Nicolas WJ / Fassler F / Dutka P / Schur FKM / Jensen GJ / Meyerowitz EM | ||||||||||||
Funding support | United States, Austria, 3 items
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Citation | Journal: Curr Biol / Year: 2022 Title: Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Authors: William J Nicolas / Florian Fäßler / Przemysław Dutka / Florian K M Schur / Grant Jensen / Elliot Meyerowitz / Abstract: One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. ...One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall's mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed "meshing," which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is-at least in part-composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at -45° and +45° relative to the cell's long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall. #1: Journal: BioRxiv / Year: 2022 Title: Bimodally oriented cellulose fibers and reticulated homogalacturonan networks - A direct visualization of Allium cepa primary cell walls Authors: Nicolas WJ / Fassler F / Dutka P / Schur FKM / Jensen GJ / Meyerowitz EM | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26569.map.gz | 489.4 MB | EMDB map data format | |
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Header (meta data) | emd-26569-v30.xml emd-26569.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_26569.png | 220.6 KB | ||
Others | emd_26569_additional_1.map.gz | 889.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26569 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26569 | HTTPS FTP |
-Validation report
Summary document | emd_26569_validation.pdf.gz | 490.6 KB | Display | EMDB validaton report |
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Full document | emd_26569_full_validation.pdf.gz | 490.2 KB | Display | |
Data in XML | emd_26569_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | emd_26569_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26569 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26569 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26569.map.gz / Format: CCP4 / Size: 787.5 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-electron tomogram of non-treated onion cell wall from scale #8 (related toFigure 3 of primary citation) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Tilt series of non-treated onion cell wall from...
File | emd_26569_additional_1.map | ||||||||||||
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Annotation | Tilt series of non-treated onion cell wall from scale #8 (related toFigure 3 of primary citation) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : primary periclinal cell wall of abaxial onion epidermal cells
Entire | Name: primary periclinal cell wall of abaxial onion epidermal cells |
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Components |
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-Supramolecule #1: primary periclinal cell wall of abaxial onion epidermal cells
Supramolecule | Name: primary periclinal cell wall of abaxial onion epidermal cells type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Allium cepa (onion) |
-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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Vitrification | Cryogen name: ETHANE-PROPANE |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.5 nA / Focused ion beam - Duration: 10 sec. / Focused ion beam - Temperature: 108 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 200 nm Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Versa 3D DualBeam. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 30 |
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