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- EMDB-53234: Amyloid structure of 17kDa alpha-amylase/trypsin inhibitor 2 (Uni... -

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Basic information

Entry
Database: EMDB / ID: EMD-53234
TitleAmyloid structure of 17kDa alpha-amylase/trypsin inhibitor 2 (Uniprot ID: AI172_ORYSJ)
Map data
Sample
  • Organelle or cellular component: Amyloid fibril of 17kDa alpha-amylase/trypsin inhibitor 2
    • Protein or peptide: 17kDa alpha-amylase/trypsin inhibitor 2
KeywordsAmyloid / Plant protein / Storage protein / Trypsin inhibitor / PROTEIN FIBRIL
Function / homologyCereal seed allergen/grain softness/trypsin and alpha-amylase inhibitor / Protease inhibitor/seed storage/LTP family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / nutrient reservoir activity / IgE binding / serine-type endopeptidase inhibitor activity / extracellular region / 17kDa alpha-amylase/trypsin inhibitor 2
Function and homology information
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodhelical reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsRhyner D / Riek R / Greenwald J / Frey L / Kwiatkowski W
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
ETH Zurich Switzerland
CitationJournal: Protein Sci / Year: 2025
Title: Impurities in amyloid studies: The power of automated model building within a cautionary tale for structural biologists.
Authors: David Rhyner / Lukas Frey / Jiangtao Zhou / Witek Kwiatkowski / Raffaele Mezzenga / Roland Riek / Jason Greenwald /
Abstract: The purity of protein samples of biological origin is often difficult to ascertain, leading the naïve or optimistic scientist to underestimate contaminants in their research. Even after extensive ...The purity of protein samples of biological origin is often difficult to ascertain, leading the naïve or optimistic scientist to underestimate contaminants in their research. Even after extensive purification, protein samples can contain nucleic acids, truncated degradation products, or other protein contaminants. While in many cases, and when present at low concentrations, such contaminants are unlikely to alter experimental results significantly, they must be considered when studying protein aggregation. Such reactions can be sensitive to small environmental changes in their early stages due to a nucleation-dependent mechanism, where minor differences can be amplified during the subsequent exponential growth phase. During a recent study of the amyloid formation of human lysozyme, we encountered a significant amyloid-forming protein contaminant derived from the expression host Oryza sativa japonica. Further investigation of this widely used commercial source of human lysozyme revealed at least a dozen protein contaminants. These discoveries led to intriguing observations, including an underdeveloped branch of plant amyloid research and a possible link between the amyloid fold and allergens. Here, we present our findings within a cautionary tale for structural biologists: a surprising variety of contaminants in a commercial protein sample and the accidental yet definitive identification of one of them by cryo-electron microscopy helical reconstruction. The resulting 2.54 Å model of the 17 kDa alpha-amylase/trypsin inhibitor Type 2 marks the first known amyloid structure of a plant protein.
History
DepositionMar 21, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53234.png

Downloads & links

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Map

FileDownload / File: emd_53234.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 512 pix.
= 332.8 Å		0.65 Å/pix.
x 512 pix.
= 332.8 Å		0.65 Å/pix.
x 512 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.0076316553 - 0.015475922
Average (Standard dev.)0.000026286736 (±0.00051143754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53234_msk_1.map
Projections & Slices
AxesZYX

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Half map: Amyloid structure of 17kDa alpha-amylase/trypsin inhibitor 2 (UNIPROT...

Fileemd_53234_half_map_1.map
AnnotationAmyloid structure of 17kDa alpha-amylase/trypsin inhibitor 2 (UNIPROT ID: AI172_ORYSJ)
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_53234_half_map_2.map
Projections & Slices
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Sample components

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Entire : Amyloid fibril of 17kDa alpha-amylase/trypsin inhibitor 2

EntireName: Amyloid fibril of 17kDa alpha-amylase/trypsin inhibitor 2
Components
  • Organelle or cellular component: Amyloid fibril of 17kDa alpha-amylase/trypsin inhibitor 2
    • Protein or peptide: 17kDa alpha-amylase/trypsin inhibitor 2

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Supramolecule #1: Amyloid fibril of 17kDa alpha-amylase/trypsin inhibitor 2

SupramoleculeName: Amyloid fibril of 17kDa alpha-amylase/trypsin inhibitor 2
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

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Macromolecule #1: 17kDa alpha-amylase/trypsin inhibitor 2

MacromoleculeName: 17kDa alpha-amylase/trypsin inhibitor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 16.493027 KDa
Recombinant expressionOrganism: Oryza sativa Japonica Group (Japanese rice)
SequenceString:
MALASDKFVL SAIVLAVLTV AAAAAGYGGY GDVGEYCRVG KAVSRNPVPS CRNYIARWCA VAGGRLDSGK QPPRQLLEPC CRELAAVPM QCRCDALSVL VRGVVTEEGD RVAGMISQHA APGCDAATIA GMASALTDYG RCNLQHTGFF GCPMFGGGMD

UniProtKB: 17kDa alpha-amylase/trypsin inhibitor 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: 7 / Details: DTT 100 mM
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 62.79 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.734 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.277 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 121923
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: generated with 2D classes as input to the program relion_helix_inimodel2d
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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