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- PDB-44zg: Sunflower protein amyloid fibrils - PM2 -

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Basic information

Entry
Database: PDB / ID: 44zg
TitleSunflower protein amyloid fibrils - PM2
Components11-S seed storage protein, plant
KeywordsPROTEIN FIBRIL / protein fibrils
Function / homology
Function and homology information


protein storage vacuole / nutrient reservoir activity / endoplasmic reticulum
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi, S. / Cao, Q. / Cao, Y.
Funding support China, 1items
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
DepositionAug 19, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 11-S seed storage protein, plant
B: 11-S seed storage protein, plant
C: 11-S seed storage protein, plant
D: 11-S seed storage protein, plant
E: 11-S seed storage protein, plant


Theoretical massNumber of molelcules
Total (without water)21,8295
Polymers21,8295
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
11-S seed storage protein, plant / Putative 11-S seed storage protein / plant / RmlC-like cupin domain / RmlC-like jelly roll fold protein


Mass: 4365.760 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helianthus annuus (common sunflower)
Gene: HannXRQ_Chr10g0288971, HannXRQ_Chr10g0301281, HanXRQr2_Chr10g0447881, HanXRQr2_Chr10g0447931
Production host: Helianthus annuus (common sunflower) / References: UniProt: A0A251TKL9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Sunflower protein amyloid fibrils PM2 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Helianthus annuus (common sunflower)
Buffer solutionpH: 2
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0.792946 ° / Axial rise/subunit: 4.78639 Å / Axial symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46925 / Symmetry type: HELICAL

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