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- EMDB-80803: Oat protein amyloid fibrils -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-80803
TitleOat protein amyloid fibrils
Map data
Sample
  • Complex: oat storage protein
    • Protein or peptide: 11S globulin
Keywordsprotein fibril
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
Biological speciesAvena sativa (oats)
Methodhelical reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsLi S / Cao Q / Cao Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Food Hydrocoll / Year: 2027
Title: Cryo-EM structure of oat amyloid fibrils reveals ordered histidine arrays on the surface
Authors: Li S / Li S / Cao Q / Fang Y / Cao Y
History
DepositionMay 9, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80803.png

Downloads & links

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Map

FileDownload / File: emd_80803.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.)
0.93 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.018850718 - 0.038040563
Average (Standard dev.)0.00008969388 (±0.0016837165)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_80803_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_80803_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 : oat storage protein

EntireName: oat storage protein
Components
  • Complex: oat storage protein
    • Protein or peptide: 11S globulin

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Supramolecule #1: oat storage protein

SupramoleculeName: oat storage protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Avena sativa (oats)

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Macromolecule #1: 11S globulin

MacromoleculeName: 11S globulin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Avena sativa (oats)
Molecular weightTheoretical: 5.142917 KDa
Recombinant expressionOrganism: Avena sativa (oats)
SequenceString:
LNIVQMSATR VNLYQNAILS PFWNINAHSV IYMIQGHARV QVVNN

UniProtKB: 11S globulin

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 2
VitrificationCryogen name: ETHANE

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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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.789 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.68385 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 171776
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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