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- EMDB-27820: Near-Atomic Resolution Structure of J-aggregated Helical Light Ha... -

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Basic information

Entry
Database: EMDB / ID: EMD-27820
TitleNear-Atomic Resolution Structure of J-aggregated Helical Light Harvesting Nanotubes
Map dataMap of C8S3 tube
Sample
  • Complex: C8S3 Double-Walled Nanotubes or Light Harvesting Nanotubes
Keywordshelical tube / helical reconstruction / CARBOHYDRATE
Biological speciesunidentified (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZheng W / Deshmukh A / Caram J / Egelman EH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Science Foundation (NSF, United States)1905242 United States
CitationJournal: 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
DepositionAug 9, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27820.png

Downloads & links

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Map

FileDownload / File: emd_27820.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of C8S3 tube
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.0368
Minimum - Maximum-0.07480128 - 0.12566704
Average (Standard dev.)0.00021100999 (±0.006931667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_27820_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_27820_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : C8S3 Double-Walled Nanotubes or Light Harvesting Nanotubes

EntireName: C8S3 Double-Walled Nanotubes or Light Harvesting Nanotubes
Components
  • Complex: C8S3 Double-Walled Nanotubes or Light Harvesting Nanotubes

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Supramolecule #1: C8S3 Double-Walled Nanotubes or Light Harvesting Nanotubes

SupramoleculeName: C8S3 Double-Walled Nanotubes or Light Harvesting Nanotubes
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: unidentified (others)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
DetailsPrepared in 30% methanol:water mixture using alcoholic route.

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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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
Final reconstructionApplied 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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