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- EMDB-50436: Cryo-EM Structure of Amyloid-beta Fibrils from Mouse Brain Carryi... -

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Basic information

Entry
Database: EMDB / ID: EMD-50436
TitleCryo-EM Structure of Amyloid-beta Fibrils from Mouse Brain Carrying the Uppsala AbetaUpp(1-42)delta(19-24) Mutation
Map datamain map, masked, symmetry applied.
Sample
  • Tissue: Amyloid fibrils of amyloid-beta(1-42)delta(19-24) extracted from mouse brain.
    • Protein or peptide: Amyloid-beta precursor protein
KeywordsAmyloid Fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


collateral sprouting in absence of injury / regulation of synapse structure or activity / axo-dendritic transport / axon midline choice point recognition / mating behavior / Golgi-associated vesicle / neuron remodeling / signaling receptor activator activity / dendrite development / regulation of multicellular organism growth ...collateral sprouting in absence of injury / regulation of synapse structure or activity / axo-dendritic transport / axon midline choice point recognition / mating behavior / Golgi-associated vesicle / neuron remodeling / signaling receptor activator activity / dendrite development / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / clathrin-coated pit / Notch signaling pathway / extracellular matrix organization / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / axonogenesis / adult locomotory behavior / central nervous system development / locomotory behavior / serine-type endopeptidase inhibitor activity / visual learning / recycling endosome / cognition / endocytosis / neuron projection development / regulation of translation / heparin binding / growth cone / perikaryon / early endosome / cell adhesion / membrane raft / axon / signaling receptor binding / apoptotic process / cell surface / endoplasmic reticulum / Golgi apparatus / DNA binding / extracellular region / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZielinski M / Peralta Reyes FS / Gremer L / Pagnon de la Vega M / Roeder C / Heidler TV / Syvaenen S / Willbold D / Sehlin D / Ingelsson M / Schroeder GF
Funding support Germany, 1 items
OrganizationGrant numberCountry
Helmholtz AssociationIVF Germany
CitationJournal: To Be Published
Title: Cryo-EM Structures of Amyloid-beta Fibrils from human and murine brains carrying the Uppsala AbetaUpp(1-42)delta(19-24) mutation
Authors: Zielinski M / Peralta Reyes FS / Gremer L / Pagnon de la Vega M / Roeder C / Heidler TV / Syvaenen S / Willbold D / Sehlin D / Ingelsson M / Schroeder GF
History
DepositionMay 26, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50436.png

Downloads & links

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Map

FileDownload / File: emd_50436.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map, masked, symmetry applied.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 300 pix.
= 242.4 Å		0.81 Å/pix.
x 300 pix.
= 242.4 Å		0.81 Å/pix.
x 300 pix.
= 242.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.029
Minimum - Maximum-0.13328013 - 0.2149604
Average (Standard dev.)0.0005931167 (±0.009811268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 242.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_50436_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_50436_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Amyloid fibrils of amyloid-beta(1-42)delta(19-24) extracted from ...

EntireName: Amyloid fibrils of amyloid-beta(1-42)delta(19-24) extracted from mouse brain.
Components
  • Tissue: Amyloid fibrils of amyloid-beta(1-42)delta(19-24) extracted from mouse brain.
    • Protein or peptide: Amyloid-beta precursor protein

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Supramolecule #1: Amyloid fibrils of amyloid-beta(1-42)delta(19-24) extracted from ...

SupramoleculeName: Amyloid fibrils of amyloid-beta(1-42)delta(19-24) extracted from mouse brain.
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse) / Organ: brain / Tissue: brain

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Macromolecule #1: Amyloid-beta precursor protein

MacromoleculeName: Amyloid-beta precursor protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Organ: brain / Tissue: brain
Molecular weightTheoretical: 3.81133 KDa
SequenceString:
DAEFRHDSGY EVHHQKLVGS NKGAIIGLMV GGVVIA

UniProtKB: Amyloid-beta precursor protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.36 Å
Applied symmetry - Helical parameters - Δ&Phi: 178.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 329437
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: a featureless cylinder with diameter of 140 Ang.
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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