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Yorodumi- EMDB-27820: Near-Atomic Resolution Structure of J-aggregated Helical Light Ha... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27820 | |||||||||
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Title | Near-Atomic Resolution Structure of J-aggregated Helical Light Harvesting Nanotubes | |||||||||
Map data | Map of C8S3 tube | |||||||||
Sample |
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Keywords | helical tube / helical reconstruction / CARBOHYDRATE | |||||||||
Biological species | unidentified (others) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Zheng W / Deshmukh A / Caram J / Egelman EH | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Chem / Year: 2024 Title: Near-atomic-resolution structure of J-aggregated helical light-harvesting nanotubes. Authors: Arundhati P Deshmukh / Weili Zheng / Chern Chuang / Austin D Bailey / Jillian A Williams / Ellen M Sletten / Edward H Egelman / Justin R Caram / Abstract: Cryo-electron microscopy has delivered a resolution revolution for biological self-assemblies, yet only a handful of structures have been solved for synthetic supramolecular materials. Particularly ...Cryo-electron microscopy has delivered a resolution revolution for biological self-assemblies, yet only a handful of structures have been solved for synthetic supramolecular materials. Particularly for chromophore supramolecular aggregates, high-resolution structures are necessary for understanding and modulating the long-range excitonic coupling. Here, we present a 3.3 Å structure of prototypical biomimetic light-harvesting nanotubes derived from an amphiphilic cyanine dye (C8S3-Cl). Helical 3D reconstruction directly visualizes the chromophore packing that controls the excitonic properties. Our structure clearly shows a brick layer arrangement, revising the previously hypothesized herringbone arrangement. Furthermore, we identify a new non-biological supramolecular motif-interlocking sulfonates-that may be responsible for the slip-stacked packing and J-aggregate nature of the light-harvesting nanotubes. This work shows how independently obtained native-state structures complement photophysical measurements and will enable accurate understanding of (excitonic) structure-function properties, informing materials design for light-harvesting chromophore aggregates. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27820.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-27820-v30.xml emd-27820.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_27820.png | 140.6 KB | ||
Filedesc metadata | emd-27820.cif.gz | 3.9 KB | ||
Others | emd_27820_half_map_1.map.gz emd_27820_half_map_2.map.gz | 49.3 MB 49.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27820 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27820 | HTTPS FTP |
-Validation report
Summary document | emd_27820_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_27820_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_27820_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_27820_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27820 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27820 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27820.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map of C8S3 tube | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map 1
File | emd_27820_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_27820_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : C8S3 Double-Walled Nanotubes or Light Harvesting Nanotubes
Entire | Name: C8S3 Double-Walled Nanotubes or Light Harvesting Nanotubes |
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Components |
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-Supramolecule #1: C8S3 Double-Walled Nanotubes or Light Harvesting Nanotubes
Supramolecule | Name: C8S3 Double-Walled Nanotubes or Light Harvesting Nanotubes type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: unidentified (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
Details | Prepared in 30% methanol:water mixture using alcoholic route. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 20.0 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: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 9.9 Å Applied symmetry - Helical parameters - Δ&Phi: 33.6 ° Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 193693 |
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Startup model | Type of model: OTHER |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION |