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- PDB-9v4f: Soy storage protein fibril (glycinin A) PM2 -

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Basic information

Entry
Database: PDB / ID: 9v4f
TitleSoy storage protein fibril (glycinin A) PM2
ComponentsGlycinin G4
KeywordsPROTEIN FIBRIL / Soy storage protein fibril
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
Biological speciesGlycine max (soybean)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsLi, S. / Cao, Q. / Cao, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)National Key R&D Program of China 2024YFF1106604 China
Ministry of Science and Technology (MoST, China)STI2030-Major Projects 2022ZD0212500 China
National Natural Science Foundation of China (NSFC)32271276 China
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: Dual Hydrophilic-Hydrophobic Core Architecture in Soy Glycinin Amyloid Fibrils Revealed by Cryo-EM.
Authors: Saiya Li / Shuangjian Li / Yijia Cheng / Yapeng Fang / Qin Cao / Yiping Cao /
Abstract: Plant-derived amyloid fibrils represent a promising class of sustainable nanomaterials outperforming their native counterparts in functionalities; however, the atomic-level structural mechanisms ...Plant-derived amyloid fibrils represent a promising class of sustainable nanomaterials outperforming their native counterparts in functionalities; however, the atomic-level structural mechanisms behind these enhancements have yet to be elucidated. Using cryo-EM, near-atomic resolution structures (3.4 and 3.5 Å) are determined for two distinct fibril polymorphs assembled in vitro from soy glycinin-A subunit. The dominant Type I fibril exhibits an unprecedented dual-core architecture, characterized by spatially segregated hydrophilic (Asp172-Asn178/Asn178'-Asp172') and hydrophobic (Val166-Ile168/Val186'-Pro184') domains, which contribute to a unique amyloid fold distinct from many known amyloid structures, including pathological and functional amyloids. In contrast, the minor Type II fibril adopts a conventional extended hydrophobic core with Tyr155-Tyr158 π-stacking. These atomic structures establish fundamental structure-property relationships that will inform the rational design of plant protein-based nanomaterials.
History
DepositionMay 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycinin G4
B: Glycinin G4
C: Glycinin G4
D: Glycinin G4
E: Glycinin G4
F: Glycinin G4
G: Glycinin G4
H: Glycinin G4
I: Glycinin G4
J: Glycinin G4


Theoretical massNumber of molelcules
Total (without water)638,75210
Polymers638,75210
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Glycinin G4 / Glycinin 11S G4 / Glycinin A5A4B3


Mass: 63875.199 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: GY4, Glyma10g04280 / Production host: Glycine max (soybean) / References: UniProt: P02858
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Soy storage protein (glycinin A) / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Glycine max (soybean)
Buffer solutionpH: 2
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
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 magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7RELION4model fitting
11RELION4classification
12RELION43D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.6 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C2
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14488 / Symmetry type: HELICAL

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