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- EMDB-64901: Cryo-EM structure of oat globulin fibril, Type 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-64901
TitleCryo-EM structure of oat globulin fibril, Type 1
Map data
Sample
  • Tissue: Cryo-EM structure of oat globulin fibril, Type 1
    • Protein or peptide: 12S seed storage globulin 2 basic chain
KeywordsPROTEIN FIBRIL / amyloid / oat globulin
Function / homology
Function and homology information


seed development / nutrient reservoir activity
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 globulin 2
Similarity search - Component
Biological speciesAvena sp. (oat) / Avena sativa (oats)
Methodhelical reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsZhang YL / Dai B
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of oat globulin fibril, Type 1
Authors: Zhang YL / Dai B
History
DepositionJun 3, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64901.png

Downloads & links

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Map

FileDownload / File: emd_64901.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0044
Minimum - Maximum-0.004713948 - 0.0097716795
Average (Standard dev.)0.000016775328 (±0.00020673739)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64901_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64901_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of oat globulin fibril, Type 1

EntireName: Cryo-EM structure of oat globulin fibril, Type 1
Components
  • Tissue: Cryo-EM structure of oat globulin fibril, Type 1
    • Protein or peptide: 12S seed storage globulin 2 basic chain

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Supramolecule #1: Cryo-EM structure of oat globulin fibril, Type 1

SupramoleculeName: Cryo-EM structure of oat globulin fibril, Type 1 / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Avena sp. (oat)

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Macromolecule #1: 12S seed storage globulin 2 basic chain

MacromoleculeName: 12S seed storage globulin 2 basic chain / type: protein_or_peptide / ID: 1
Details: The protein that forms fibrils is 12S globulin, which is derived from oat.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Avena sativa (oats)
Molecular weightTheoretical: 4.055648 KDa
SequenceString:
VNLYQNAILS PYWNINAHSV MHMIQGRARV QVVNN

UniProtKB: 12S seed storage globulin 2

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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: 2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.58 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 22559
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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