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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: To Be Published
Title: Amyloid structure of 17kDa alpha-amylase/trypsin inhibitor 2 (Uniprot ID: AI172_ORYSJ)
Authors: Rhyner D / Riek R / Greenwald J / Frey L / Kwiatkowski W
History
DepositionMar 21, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 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
Brightness
Contrast
Others
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)

Slices (2/3)

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53234_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 : 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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