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- PDB-9oig: Structure of Type II ABri amyloid filaments extracted from human ... -

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Basic information

Entry
Database: PDB / ID: 9oig
TitleStructure of Type II ABri amyloid filaments extracted from human brain of Familial British Dementia patient
Components
  • ABri (ITM2B mutant)
  • unknown protein
KeywordsPROTEIN FIBRIL / amyloid / filament / neurodegeneration / brain / ex vivo
Function / homologyRNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsOzcan, K.A. / Vago, F. / Bharath, S.R. / Jiang, W. / Vidal, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: To Be Published
Title: Cryo-EM structures of ADan and ABri filaments from FDD and FBD
Authors: Ozcan, K.A. / Vago, F. / Bharath, S.R. / Jiang, W. / Vidal, R.
History
DepositionMay 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 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
A: ABri (ITM2B mutant)
B: ABri (ITM2B mutant)
C: ABri (ITM2B mutant)
D: ABri (ITM2B mutant)
E: ABri (ITM2B mutant)
F: ABri (ITM2B mutant)
G: ABri (ITM2B mutant)
H: ABri (ITM2B mutant)
I: ABri (ITM2B mutant)
J: ABri (ITM2B mutant)
K: unknown protein
L: unknown protein
M: unknown protein
N: unknown protein
O: unknown protein


Theoretical massNumber of molelcules
Total (without water)39,51615
Polymers39,51615
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
ABri (ITM2B mutant)


Mass: 3676.227 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: RNA chain
unknown protein


Mass: 550.776 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
Has protein modificationY

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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: ABri amyloid filament / Type: TISSUE / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.08 ° / Axial rise/subunit: 4.77 Å / Axial symmetry: C1
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24596 / Symmetry type: HELICAL

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