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- EMDB-25795: Structure of In-vitro Synthesized Cellulose Fibrils by Averaging ... -

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Entry
Database: EMDB / ID: EMD-25795
TitleStructure of In-vitro Synthesized Cellulose Fibrils by Averaging non-overlapping subtograms of 10.9x26.5x10.9 nm
Map dataAverage of 10.9x26.5x10.9 nm subtograms of in-vitro synthesized cellulose fibrils.
Sample
  • Organelle or cellular component: In-vitro synthesized cellulose microfibril
Keywordscellulose / microfibril / in-vitro synthesized / CARBOHYDRATE
Biological speciesPhyscomitrium patens (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 23.0 Å
AuthorsNixon BT / Frank MA
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0001090 United States
CitationJournal: Biomacromolecules / Year: 2022
Title: Structure of -Synthesized Cellulose Fibrils Viewed by Cryo-Electron Tomography and C Natural-Abundance Dynamic Nuclear Polarization Solid-State NMR.
Authors: Fabien Deligey / Mark A Frank / Sung Hyun Cho / Alex Kirui / Frederic Mentink-Vigier / Matthew T Swulius / B Tracy Nixon / Tuo Wang /
Abstract: Cellulose, the most abundant biopolymer, is a central source for renewable energy and functionalized materials. synthesis of cellulose microfibrils (CMFs) has become possible using purified ...Cellulose, the most abundant biopolymer, is a central source for renewable energy and functionalized materials. synthesis of cellulose microfibrils (CMFs) has become possible using purified cellulose synthase (CESA) isoforms from and hybrid aspen. The exact nature of these fibrils remains unknown. Here, we characterize -synthesized fibers made by CESAs present in membrane fractions of over-expressing CESA5 by cryo-electron tomography and dynamic nuclear polarization (DNP) solid-state NMR. DNP enabled measuring two-dimensional C-C correlation spectra without isotope-labeling of the fibers. Results show structural similarity between fibrils and native CMF in plant cell walls. Intensity quantifications agree with the 18-chain structural model for plant CMF and indicate limited fibrillar bundling. The system thus reveals insights into cell wall synthesis and may contribute to novel cellulosic materials. The integrated DNP and cryo-electron tomography methods are also applicable to structural studies of other carbohydrate-based biomaterials.
History
DepositionDec 21, 2021-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25795.png

Downloads & links

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Map

FileDownload / File: emd_25795.map.gz / Format: CCP4 / Size: 1.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAverage of 10.9x26.5x10.9 nm subtograms of in-vitro synthesized cellulose fibrils.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.1 Å/pix.
x 48 pix.
= 100.896 Å		2.1 Å/pix.
x 126 pix.
= 264.852 Å		2.1 Å/pix.
x 48 pix.
= 100.896 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.102 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 121.0
Minimum - Maximum117.998900000000006 - 133.603870000000001
Average (Standard dev.)124.781660000000002 (±2.9628575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1264848
Spacing4812648
CellA: 100.895996 Å / B: 264.852 Å / C: 100.895996 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : In-vitro synthesized cellulose microfibril

EntireName: In-vitro synthesized cellulose microfibril
Components
  • Organelle or cellular component: In-vitro synthesized cellulose microfibril

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Supramolecule #1: In-vitro synthesized cellulose microfibril

SupramoleculeName: In-vitro synthesized cellulose microfibril / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 5.4 kDa/nm

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -5.0 µm / Nominal defocus min: -5.0 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.658 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 12 / Number images used: 4384
Final angle assignmentType: PROJECTION MATCHING / Software - Name: IMOD (ver. 4.12.8) / Software - details: 3dmod
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.15.1) / Number subtomograms used: 4374

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