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- EMDB-61851: Cryo-EM of Zingibroside R1 nanofibrils -

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Basic information

Entry
Database: EMDB / ID: EMD-61851
TitleCryo-EM of Zingibroside R1 nanofibrils
Map dataMap (not sharpened)
Sample
  • Organelle or cellular component: Zingibroside R1
KeywordsZingibroside R1 / Hydrogel / Antifungal / Traditional Chinese Medicine. / UNKNOWN FUNCTION
Biological speciesPanax japonicus (chikusetu-ninjin)
Methodhelical reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsPeng Q / Song H
Funding supportMacao, 1 items
OrganizationGrant numberCountry
Other government0068/2023/ITP2Macao
CitationJournal: Adv Mater / Year: 2025
Title: Atomic Insights Into Self-Assembly of Zingibroside R1 and its Therapeutic Action Against Fungal Diseases.
Authors: Mengyun Peng / Qiwei Peng / Wei Li / Xiaochun Chen / Qipeng Yan / Xia Wu / Mingxing Wu / Dan Yuan / He Song / Junfeng Shi /
Abstract: Natural products are a crucial resource for drug discovery, but poor understanding of the molecular-scale mechanisms of their self-assembly into soluble, bioavailable hydrogels limits their ...Natural products are a crucial resource for drug discovery, but poor understanding of the molecular-scale mechanisms of their self-assembly into soluble, bioavailable hydrogels limits their applications and therapeutic potential. It is demonstrated that Zingibroside R1 (ZR1), derived from Panax notoginseng, undergoes spontaneous self-assemble into a hydrogel comprising helical nanofibrils with potent antifungal activity lacking in its monomeric state. Cryogenic electron microscopy (cryo-EM) revealed an intricate hydrogen-bonding network that facilitates ZR1 nanofibril formation, characterized by a hydrophobic core and hydrophilic exterior architecture, which underpin its binding activity with cell wall in the vulvovaginal candidiasis (VVC) pathogen, C. albicans. The hydrogen-bonding interface between ZR1 gel and glucan compromises membrane integrity, inhibiting C. albicans proliferation in vitro and in VVC model mice in vivo. ZR1 gel could also deliver probiotic Lactobacillus, synergistically inhibiting VVC and restoring the vaginal microenvironment. This study advances the mechanistic understanding of ZR1's structure-function relationships, offering valuable insights into the rational design and therapeutic optimization of natural product-based hydrogels.
History
DepositionOct 10, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61851.png

Downloads & links

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Map

FileDownload / File: emd_61851.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap (not sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å

Surface

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.22033271 - 0.94161355
Average (Standard dev.)0.001642343 (±0.0348215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_61851_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_61851_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_61851_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Zingibroside R1

EntireName: Zingibroside R1
Components
  • Organelle or cellular component: Zingibroside R1

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Supramolecule #1: Zingibroside R1

SupramoleculeName: Zingibroside R1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Panax japonicus (chikusetu-ninjin)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7 / Details: PBS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.68 Å
Applied symmetry - Helical parameters - Δ&Phi: -93.94 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6) / Number images used: 959637
CTF correctionSoftware - Name: cryoSPARC (ver. v4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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