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- EMDB-65825: Structure of type II Abeta fibrils from 5xFAD mice -

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Basic information

Entry
Database: EMDB / ID: EMD-65825
TitleStructure of type II Abeta fibrils from 5xFAD mice
Map data
Sample
  • Tissue: Type II Amyloid-beta fibrils from 5xFAD mice
    • Protein or peptide: Amyloid-beta protein 42
KeywordsAbeta / amyloid / cryo-EM / PROTEIN FIBRIL
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / Aggregated β-amyloid induces FXII autocatalysis / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / hippocampal neuron apoptotic process / microglia development / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands ...amyloid-beta complex / growth cone lamellipodium / Aggregated β-amyloid induces FXII autocatalysis / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / hippocampal neuron apoptotic process / microglia development / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / Aggregated β-amyloid interacts with fibrinogen / axon midline choice point recognition / regulation of synapse structure or activity / positive regulation of synaptic transmission, cholinergic / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / nuclear envelope lumen / growth factor receptor binding / peptidase activator activity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / PTB domain binding / Golgi-associated vesicle / Lysosome Vesicle Biogenesis / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / astrocyte projection / regulation of multicellular organism growth / dendrite development / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / negative regulation of long-term synaptic potentiation / signaling receptor activator activity / transition metal ion binding / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / intracellular copper ion homeostasis / modulation of excitatory postsynaptic potential / ECM proteoglycans / main axon / response to insulin-like growth factor stimulus / positive regulation of T cell migration / extracellular matrix organization / adult locomotory behavior / swimming behavior / regulation of presynapse assembly / regulation of long-term neuronal synaptic plasticity / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / positive regulation of chemokine production / axonogenesis / cellular response to manganese ion / cellular response to cAMP / neuron projection maintenance / clathrin-coated pit / positive regulation of glycolytic process / visual learning / synaptic cleft / astrocyte activation / Mitochondrial protein degradation / locomotory behavior / platelet alpha granule lumen / regulation of neuron apoptotic process / ionotropic glutamate receptor signaling pathway / response to interleukin-1 / learning / endosome lumen / cellular response to copper ion / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / serine-type endopeptidase inhibitor activity / Regulation of clotting cascade / protein serine/threonine kinase binding / endocytosis / Post-translational protein phosphorylation / trans-Golgi network membrane / dendritic shaft / cellular response to nerve growth factor stimulus / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of JNK cascade / positive regulation of interleukin-6 production / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / Golgi lumen / recycling endosome / response to lead ion / cognition / regulation of translation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / regulation of gene expression / calcium ion transport / heparin binding
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, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...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, heparin-binding / Amyloid A4 N-terminal heparin-binding / 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, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / 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) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCao Q / Song M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Abeta fibrils from brains of 5xFAD and AppNL-FPsen1P117L mice adopt human Type II fibril fold as revealed by cryo-EM
Authors: Cao Q / Zhang D / Song M / Zheng H / Han J / Xu K
History
DepositionAug 12, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65825.png

Downloads & links

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Map

FileDownload / File: emd_65825.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesX (Sec.)Y (Row.)Z (Col.)
0.93 Å/pix.
x 150 pix.
= 139.8 Å		0.93 Å/pix.
x 150 pix.
= 139.8 Å		0.93 Å/pix.
x 150 pix.
= 139.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-6.431982 - 11.246316999999999
Average (Standard dev.)-0.000000000019455 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-75-75-75
Dimensions150150150
Spacing150150150
CellA=B=C: 139.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65825_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65825_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Type II Amyloid-beta fibrils from 5xFAD mice

EntireName: Type II Amyloid-beta fibrils from 5xFAD mice
Components
  • Tissue: Type II Amyloid-beta fibrils from 5xFAD mice
    • Protein or peptide: Amyloid-beta protein 42

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Supramolecule #1: Type II Amyloid-beta fibrils from 5xFAD mice

SupramoleculeName: Type II Amyloid-beta fibrils from 5xFAD mice / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Amyloid-beta protein 42

MacromoleculeName: Amyloid-beta protein 42 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.520087 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

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: 7.4
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: 3.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.77 Å
Applied symmetry - Helical parameters - Δ&Phi: -3.2 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 25555
CTF correctionType: NONE
Segment selectionNumber selected: 426271 / Software - Name: Topaz (ver. v0.2.5)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7q4m

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9wao:
Structure of type II Abeta fibrils from 5xFAD mice

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