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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: 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, 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
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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