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- EMDB-64767: Soy storage protein fibril (glycinin A) PM1 -

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Basic information

Entry
Database: EMDB / ID: EMD-64767
TitleSoy storage protein fibril (glycinin A) PM1
Map data
Sample
  • Complex: soy protein(Glycine max)
    • Protein or peptide: Glycinin G4
Keywordsdual hydrophilic-hydrophobic / 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)
Methodhelical reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsLi S / Cao Q / Cao Y
Funding support China, 3 items
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 22, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64767.png

Downloads & links

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Map

FileDownload / File: emd_64767.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-18.625443000000001 - 27.392219999999998
Average (Standard dev.)0.000000000004253 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_64767_msk_1.map
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Half map: #2

Fileemd_64767_half_map_1.map
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Half map: #1

Fileemd_64767_half_map_2.map
Projections & Slices
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Sample components

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Entire : soy protein(Glycine max)

EntireName: soy protein(Glycine max)
Components
  • Complex: soy protein(Glycine max)
    • Protein or peptide: Glycinin G4

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Supramolecule #1: soy protein(Glycine max)

SupramoleculeName: soy protein(Glycine max) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Glycine max (soybean)

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Macromolecule #1: Glycinin G4

MacromoleculeName: Glycinin G4 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Glycine max (soybean)
Molecular weightTheoretical: 63.875199 KDa
Recombinant expressionOrganism: Glycine max (soybean)
SequenceString: MGKPFTLSLS SLCLLLLSSA CFAISSSKLN ECQLNNLNAL EPDHRVESEG GLIQTWNSQH PELKCAGVTV SKLTLNRNGL HLPSYSPYP RMIIIAQGKG ALGVAIPGCP ETFEEPQEQS NRRGSRSQKQ QLQDSHQKIR HFNEGDVLVI PPGVPYWTYN T GDEPVVAI ...String:
MGKPFTLSLS SLCLLLLSSA CFAISSSKLN ECQLNNLNAL EPDHRVESEG GLIQTWNSQH PELKCAGVTV SKLTLNRNGL HLPSYSPYP RMIIIAQGKG ALGVAIPGCP ETFEEPQEQS NRRGSRSQKQ QLQDSHQKIR HFNEGDVLVI PPGVPYWTYN T GDEPVVAI SLLDTSNFNN QLDQTPRVFY LAGNPDIEYP ETMQQQQQQK SHGGRKQGQH QQEEEEEGGS VLSGFSKHFL AQ SFNTNED IAEKLQSPDD ERKQIVTVEG GLSVISPKWQ EQQDEDEDED EDDEDEQIPS HPPRRPSHGK REQDEDEDED EDK PRPSRP SQGKREQDQD QDEDEDEDED QPRKSREWRS KKTQPRRPRQ EEPRERGCET RNGVEENICT LKLHENIARP SRAD FYNPK AGRISTLNSL TLPALRQFQL SAQYVVLYKN GIYSPHWNLN ANSVIYVTRG QGKVRVVNCQ GNAVFDGELR RGQLL VVPQ NFVVAEQAGE QGFEYIVFKT HHNAVTSYLK DVFRAIPSEV LAHSYNLRQS QVSELKYEGN WGPLVNPESQ QGSPRV KVA

UniProtKB: Glycinin G4

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

Concentration20 mg/mL
BufferpH: 2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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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 opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.466 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 71617
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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