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- EMDB-26573: Subtomogram average of a pectate lyase cellulose fiber (related t... -

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Basic information

Entry
Database: EMDB / ID: EMD-26573
TitleSubtomogram average of a pectate lyase cellulose fiber (related to Figure 7C of primary citation)
Map dataSubtomogram average of a pectate lyase cellulose fiber (related to Figure 7C of primary citation)
Sample
  • Cell: Onion epidermal periclinal cell wall
Biological speciesAllium cepa (onion)
Methodsubtomogram averaging / cryo EM
AuthorsNicolas WJ / Fassler F / Dutka P / Schur FKM / Jensen GJ / Meyerowitz EM
Funding support United States, Austria, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122588 United States
Austrian Science FundP33367 Austria
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
DepositionMar 31, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26573.png

Downloads & links

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Map

FileDownload / File: emd_26573.map.gz / Format: CCP4 / Size: 251 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of a pectate lyase cellulose fiber (related to Figure 7C of primary citation)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.66 Å/pix.
x 40 pix.
= 266.56 Å		6.66 Å/pix.
x 40 pix.
= 266.56 Å		6.66 Å/pix.
x 40 pix.
= 266.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.75
Minimum - Maximum-2.6191504 - 4.577706
Average (Standard dev.)0.0060796556 (±0.58357817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-20-20-20
Dimensions404040
Spacing404040
CellA=B=C: 266.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_26573_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26573_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Onion epidermal periclinal cell wall

EntireName: Onion epidermal periclinal cell wall
Components
  • Cell: Onion epidermal periclinal cell wall

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Supramolecule #1: Onion epidermal periclinal cell wall

SupramoleculeName: Onion epidermal periclinal cell wall / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Allium cepa (onion)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 10.0 µm / Nominal defocus min: 10.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber subtomograms used: 30
ExtractionNumber tomograms: 1100 / Number images used: 1100

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