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- PDB-9vam: Cryo-EM structure of oat globulin fibril, Type 1 -

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Basic information

Entry
Database: PDB / ID: 9vam
TitleCryo-EM structure of oat globulin fibril, Type 1
Components12S seed storage globulin 2 basic chain
KeywordsPROTEIN FIBRIL / amyloid / oat globulin
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
12S seed storage globulin 2
Similarity search - Component
Biological speciesAvena sativa (oats)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsZhang, Y.L. / Dai, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of oat globulin fibril, Type 1
Authors: Zhang, Y.L. / Dai, B.
History
DepositionJun 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data 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
AC: 12S seed storage globulin 2 basic chain
AA: 12S seed storage globulin 2 basic chain
AB: 12S seed storage globulin 2 basic chain


Theoretical massNumber of molelcules
Total (without water)12,1673
Polymers12,1673
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/peptide 12S seed storage globulin 2 basic chain


Mass: 4055.648 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: The protein that forms fibrils is 12S globulin, which is derived from oat.
Source: (natural) Avena sativa (oats) / References: UniProt: P14812
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: Cryo-EM structure of oat globulin fibril, Type 1 / Type: TISSUE / Entity ID: all / Source: NATURAL
Source (natural)Organism: Avena sp. (oat)
Buffer solutionpH: 2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
9PHENIX1.15.2_3472model refinement
13RELION3D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -1.58 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C1
3D reconstructionResolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22559 / Symmetry type: HELICAL
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0052870
ELECTRON MICROSCOPYf_angle_d0.95231185
ELECTRON MICROSCOPYf_chiral_restr0.0751132
ELECTRON MICROSCOPYf_plane_restr0.0101153
ELECTRON MICROSCOPYf_dihedral_angle_d18.3401513

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