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- EMDB-80851: Sunflower protein amyloid fibrils -

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Basic information

Entry
Database: EMDB / ID: EMD-80851
TitleSunflower protein amyloid fibrils
Map data
Sample
  • Complex: Sunflower storage protein
    • Complex: Sunflower storage protein
      • Protein or peptide: 11-S seed storage protein, plant
Keywordsprotein fibril
Function / homology
Function and homology information


nutrient reservoir activity
Similarity search - Function
11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
11-S seed storage protein, plant
Similarity search - Component
Biological speciesHelianthus annuus (common sunflower)
Methodhelical reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsLi S / Cao Q / Cao Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32572505 China
CitationJournal: Small / Year: 2026
Title: Cryo-EM Structures of Sunflower Amyloid Fibrils Reveal Two Distinct Disulfide‑Linked Assembly Modes.
Authors: Saiya Li / Kefan Ouyang / Shuangjian Li / Yapeng Fang / Qin Cao / Yiping Cao /
Abstract: Sunflower meal is an abundant but underutilized plant protein source. Recent studies have demonstrated that its amyloid fibrils exhibit exceptional functional properties, yet the atomic-level ...Sunflower meal is an abundant but underutilized plant protein source. Recent studies have demonstrated that its amyloid fibrils exhibit exceptional functional properties, yet the atomic-level structural basis remains unknown. The first cryo‑electron microscopy (cryo‑EM) structures of sunflower amyloid fibrils prepared under acidic heating conditions are presented. Two distinct polymorphs (PM1 and PM2) are resolved at 3.05 and 3.18 Å, respectively. They differ markedly in both helical half-pitch (389 Å for PM1 vs. 1087 Å for PM2) and handedness (left-handed for PM1 vs. right-handed for PM2). High-resolution atomic modeling reveals that they adopt distinct assembly modes. PM1 is assembled from the acidic (Leu94-Phe115) and basic (Val333-Phe344) subunits of 11S globulin, covalently linked by an inter-subunit disulfide bond (Cys111-Cys338); whereas PM2 is formed by an acidic-subunit segment (Asn30-Val68) and stabilized by an intra-subunit disulfide bond (Cys32-Cys65). Comparison of the PM1 structure with the apricot globulin fibril reveals divergent assembly strategies, most strikingly an opposite orientation of the basic subunit relative to the acidic fragment despite high sequence homology. These structural insights provide a molecular foundation for understanding and engineering sunflower amyloid fibrils for diverse applications in food, agriculture, and nanotechnology.
History
DepositionMay 13, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80851.png

Downloads & links

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Map

FileDownload / File: emd_80851.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.016489096 - 0.038791653
Average (Standard dev.)0.00018738631 (±0.0017455646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 335.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80851_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80851_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Sunflower storage protein

EntireName: Sunflower storage protein
Components
  • Complex: Sunflower storage protein
    • Complex: Sunflower storage protein
      • Protein or peptide: 11-S seed storage protein, plant

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Supramolecule #1: Sunflower storage protein

SupramoleculeName: Sunflower storage protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helianthus annuus (common sunflower)

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Supramolecule #2: Sunflower storage protein

SupramoleculeName: Sunflower storage protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Helianthus annuus (common sunflower)

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Macromolecule #1: 11-S seed storage protein, plant

MacromoleculeName: 11-S seed storage protein, plant / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Helianthus annuus (common sunflower)
Molecular weightTheoretical: 28.54125 KDa
Recombinant expressionOrganism: Helianthus annuus (common sunflower)
SequenceString: LLFIEQGEGI VGIQLPGCAE TFDTGVQQQH MQQQQQHQQQ QQQQQQQQQP RRMGERGMDS SADSHQKVHR FREGDIIAIP AGAVYWTYN DRNQEVVAII VDDVNNPANQ LDFQAKTSFL AGGISSEHIQ GQQQFQGQQG RQGQQQIHGQ QSRQQGRQQG R RRSPFGGQ ...String:
LLFIEQGEGI VGIQLPGCAE TFDTGVQQQH MQQQQQHQQQ QQQQQQQQQP RRMGERGMDS SADSHQKVHR FREGDIIAIP AGAVYWTYN DRNQEVVAII VDDVNNPANQ LDFQAKTSFL AGGISSEHIQ GQQQFQGQQG RQGQQQIHGQ QSRQQGRQQG R RRSPFGGQ EELTRDNVYA GFDTELLAEA FNCDPQIMRA LQESRNRGVI VQVQQQMEFV TPEEEQQQMH QRRSRGGPSN GV EETICSA KLVF

UniProtKB: 11-S seed storage protein, plant

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 2
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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.757 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.2017 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 296338
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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