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- PDB-9qlu: Amyloid structure of 17kDa alpha-amylase/trypsin inhibitor 2 (Uni... -

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Basic information

Entry
Database: PDB / ID: 9qlu
TitleAmyloid structure of 17kDa alpha-amylase/trypsin inhibitor 2 (Uniprot ID: AI172_ORYSJ)
Components17kDa alpha-amylase/trypsin inhibitor 2
KeywordsPROTEIN FIBRIL / Amyloid / Plant protein / Storage protein / Trypsin inhibitor
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsRhyner, D. / Riek, R. / Greenwald, J. / Frey, L. / Kwiatkowski, W.
Funding support Switzerland, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17kDa alpha-amylase/trypsin inhibitor 2
B: 17kDa alpha-amylase/trypsin inhibitor 2
C: 17kDa alpha-amylase/trypsin inhibitor 2
D: 17kDa alpha-amylase/trypsin inhibitor 2
E: 17kDa alpha-amylase/trypsin inhibitor 2


Theoretical massNumber of molelcules
Total (without water)82,4655
Polymers82,4655
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 16493.027 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os07g0216700, LOC_Os07g11650, OJ1080_F08.106, OJ1779_B07.133, OsJ_23556
Production host: Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q7X8H9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Amyloid fibril of 17kDa alpha-amylase/trypsin inhibitor 2
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Buffer solutionpH: 7 / Details: DTT 100 mM
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 288.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 62.79 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM softwareName: RELION / Version: 4.0.0 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -2.277 ° / Axial rise/subunit: 4.734 Å / Axial symmetry: C1
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121923 / Symmetry type: HELICAL

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