9V4F | pdb_00009v4f

Soy storage protein fibril (glycinin A) PM2

  • Classification: PROTEIN FIBRIL
  • Organism(s): Glycine max
  • Expression System: Glycine max
  • Mutation(s): No 

  • Deposited: 2025-05-23 Released: 2025-09-10 
  • Deposition Author(s): Li, S., Cao, Q., Cao, Y.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dual Hydrophilic-Hydrophobic Core Architecture in Soy Glycinin Amyloid Fibrils Revealed by Cryo-EM.

Li, S.Li, S.Cheng, Y.Fang, Y.Cao, Q.Cao, Y.

(2025) Adv Sci (Weinh) 12: e09821-e09821

  • DOI: https://doi.org/10.1002/advs.202509821
  • Primary Citation of Related Structures:  
    9V45, 9V4F

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Department of Food Science & Engineering, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycinin G4
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
563Glycine maxMutation(s): 0 
Gene Names: GY4Glyma10g04280
UniProt
Find proteins for P02858 (Glycine max)
Explore P02858 
Go to UniProtKB:  P02858
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02858
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)ChinaNational Key R&D Program of China 2024YFF1106604
Ministry of Science and Technology (MoST, China)ChinaSTI2030-Major Projects 2022ZD0212500
National Natural Science Foundation of China (NSFC)China32271276

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-11-26
    Changes: Data collection, Database references