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- EMDB-53117: LY12 Main Morphology -

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Basic information

Entry
Database: EMDB / ID: EMD-53117
TitleLY12 Main Morphology
Map dataMap of LY12 fibril reconstruction.
Sample
  • Complex: Amyloid fibril formed by the aggregation of a 12 aa long fragment from cruciferin 3 (223-234) from A. thaliana.
    • Protein or peptide: 12S seed storage protein CRC alpha chain
Keywordsamyloid fibril / seed storage protein / in vitro / PROTEIN FIBRIL
Function / homology
Function and homology information


seed maturation / cellular response to abscisic acid stimulus / protein storage vacuole / nutrient reservoir activity / response to abscisic acid
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
12S seed storage protein CRC
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodhelical reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsStoyanov N / Schmidt M / Faendrich M
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
iNEXT-DiscoveryEuropean Union
German Research Foundation (DFG) Germany
CitationJournal: Int J Biol Macromol / Year: 2026
Title: A fragment of 12S seed storage protein of Arabidopsis forms twisted cross beta-sheet rich amyloid fibrils.
Authors: Vijay Kumar / Nikolay Stoyanov / Vibha Kaushik / Sourav Kumar / Matthias Schmidt / Marcus Fändrich / Daniel Segal /
Abstract: Plant seed storage proteins (SSPs) serve as a nutrient source and are suggested to be crucial for seed survival during dormancy and desiccation. They form highly stable and environmentally stress- ...Plant seed storage proteins (SSPs) serve as a nutrient source and are suggested to be crucial for seed survival during dormancy and desiccation. They form highly stable and environmentally stress-resistant amyloid structures. SSP amyloids are gaining significant attention for fabricating sustainable biomaterials in recent times; however, the requirement for optimized fibrillation conditions limits their practical use. Therefore, understanding the molecular mechanism of SSP amyloidogenesis, biochemical conditions, and the biophysical properties of the resultant amyloid fibrils becomes crucial. This study investigates the amyloidogenic properties of Cruciferin-3 (CRU-3), a major SSP from Arabidopsis thaliana, focusing on the 12-residue representative peptide, L-Y (LY12), computationally predicted to be amyloidogenic. LY12 forms β-sheet rich amyloid fibrils in a nucleation-dependent manner in vitro with the potential to seed self-aggregation. The peptide fibrillation was found to be pH-dependent and showed a moderate resistance to Proteinase-K treatment. Molecular-level insight into the structure of LY12 fibrils was obtained using cryogenic-electron microscopy (cryo-EM) at a high resolution of 2.86 Å. The structure of LY12 fibrils revealed a C2 symmetrical, left-handed, twisted core comprising three non-equivalent peptide stacks. This unique cross β-sheet dense core, stabilized by hydrophobic and electrostatic interactions, and surrounded by low-density peptide layers, distinguishes them from pathological amyloids. This study explores the conditions for LY12 amyloid formation and deciphers their biophysical attributes and structural details, suggesting the potential physiological roles and biomaterial applications of CRU-3 amyloids.
History
DepositionMar 12, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53117.png

Downloads & links

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Map

FileDownload / File: emd_53117.map.gz / Format: CCP4 / Size: 16.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of LY12 fibril reconstruction.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 50 pix.
= 36.55 Å		0.73 Å/pix.
x 300 pix.
= 219.3 Å		0.73 Å/pix.
x 295 pix.
= 215.645 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00125
Minimum - Maximum-0.0028625384 - 0.0048865234
Average (Standard dev.)0.000017683407 (±0.00028531763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin05134
Dimensions30029550
Spacing29530050
CellA: 215.645 Å / B: 219.3 Å / C: 36.55 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53117_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map 1 of LY12 fibril reconstruction.

Fileemd_53117_half_map_1.map
AnnotationUnfiltered half-map 1 of LY12 fibril reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map 2 of LY12 fibril reconstruction.

Fileemd_53117_half_map_2.map
AnnotationUnfiltered half-map 2 of LY12 fibril reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Amyloid fibril formed by the aggregation of a 12 aa long fragment...

EntireName: Amyloid fibril formed by the aggregation of a 12 aa long fragment from cruciferin 3 (223-234) from A. thaliana.
Components
  • Complex: Amyloid fibril formed by the aggregation of a 12 aa long fragment from cruciferin 3 (223-234) from A. thaliana.
    • Protein or peptide: 12S seed storage protein CRC alpha chain

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Supramolecule #1: Amyloid fibril formed by the aggregation of a 12 aa long fragment...

SupramoleculeName: Amyloid fibril formed by the aggregation of a 12 aa long fragment from cruciferin 3 (223-234) from A. thaliana.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: 12S seed storage protein CRC alpha chain

MacromoleculeName: 12S seed storage protein CRC alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 1.330613 KDa
SequenceString:
LVIIALLDIA NY

UniProtKB: 12S seed storage protein CRC

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.2
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 6.0 sec. / Average electron dose: 52.29 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.78 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.66 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 134959
CTF correctionSoftware - Name: RELION (ver. 5.0-beta) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 5.0-beta)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9qfm:
LY12 Main Morphology

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