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- PDB-9oi9: Structure of ADan amyloid filaments extracted from human brain of... -

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Basic information

Entry
Database: PDB / ID: 9oi9
TitleStructure of ADan amyloid filaments extracted from human brain of Familial Danish Dementia patient
ComponentsADan (ITM2B mutant)
KeywordsPROTEIN FIBRIL / amyloid / filament / neurodegeneration / brain / ex vivo
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsOzcan, K.A. / Vago, F. / 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. / 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: ADan (ITM2B mutant)
B: ADan (ITM2B mutant)
C: ADan (ITM2B mutant)
D: ADan (ITM2B mutant)
E: ADan (ITM2B mutant)
F: ADan (ITM2B mutant)
G: ADan (ITM2B mutant)
H: ADan (ITM2B mutant)
I: ADan (ITM2B mutant)
J: ADan (ITM2B mutant)
K: ADan (ITM2B mutant)
L: ADan (ITM2B mutant)
M: ADan (ITM2B mutant)
N: ADan (ITM2B mutant)
O: ADan (ITM2B mutant)


Theoretical massNumber of molelcules
Total (without water)44,70715
Polymers44,70715
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
ADan (ITM2B mutant)


Mass: 2980.483 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: Brain
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: ADan 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: -1.48 ° / Axial rise/subunit: 4.79 Å / Axial symmetry: C3
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117271 / Symmetry type: HELICAL

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