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Yorodumi- EMDB-25795: Structure of In-vitro Synthesized Cellulose Fibrils by Averaging ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25795 | |||||||||
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Title | Structure of In-vitro Synthesized Cellulose Fibrils by Averaging non-overlapping subtograms of 10.9x26.5x10.9 nm | |||||||||
Map data | Average of 10.9x26.5x10.9 nm subtograms of in-vitro synthesized cellulose fibrils. | |||||||||
Sample |
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Keywords | cellulose / microfibril / in-vitro synthesized / CARBOHYDRATE | |||||||||
Biological species | Physcomitrium patens (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 23.0 Å | |||||||||
Authors | Nixon BT / Frank MA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25795.map.gz | 904.8 KB | EMDB map data format | |
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Header (meta data) | emd-25795-v30.xml emd-25795.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_25795.png | 48.4 KB | ||
Filedesc metadata | emd-25795.cif.gz | 4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25795 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25795 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25795.map.gz / Format: CCP4 / Size: 1.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Average of 10.9x26.5x10.9 nm subtograms of in-vitro synthesized cellulose fibrils. | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.102 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : In-vitro synthesized cellulose microfibril
Entire | Name: In-vitro synthesized cellulose microfibril |
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Components |
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-Supramolecule #1: In-vitro synthesized cellulose microfibril
Supramolecule | Name: In-vitro synthesized cellulose microfibril / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Physcomitrium patens (plant) |
Molecular weight | Theoretical: 5.4 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.658 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -5.0 µm / Nominal defocus min: -5.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied 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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Extraction | Number tomograms: 12 / Number images used: 4384 |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: IMOD (ver. 4.12.8) / Software - details: 3dmod |