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- PDB-9fh1: Cryo-EM Structure of Amyloid-beta Fibrils from Mouse Brain Carryi... -

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Basic information

Entry
Database: PDB / ID: 9fh1
TitleCryo-EM Structure of Amyloid-beta Fibrils from Mouse Brain Carrying the Uppsala AbetaUpp(1-42)delta(19-24) Mutation
ComponentsAmyloid-beta precursor protein
KeywordsPROTEIN FIBRIL / Amyloid 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 / dendrite development / signaling receptor activator activity / 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 / dendrite development / signaling receptor activator activity / 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZielinski, M. / Peralta Reyes, F.S. / Gremer, L. / Pagnon de la Vega, M. / Roeder, C. / Heidler, T.V. / Syvaenen, S. / Willbold, D. / Sehlin, D. / Ingelsson, M. / Schroeder, G.F.
Funding support Germany, 1items
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, F.S. / Gremer, L. / Pagnon de la Vega, M. / Roeder, C. / Heidler, T.V. / Syvaenen, S. / Willbold, D. / Sehlin, D. / Ingelsson, M. / Schroeder, G.F.
History
DepositionMay 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid-beta precursor protein
B: Amyloid-beta precursor protein
C: Amyloid-beta precursor protein
D: Amyloid-beta precursor protein
E: Amyloid-beta precursor protein
F: Amyloid-beta precursor protein
G: Amyloid-beta precursor protein
H: Amyloid-beta precursor protein
I: Amyloid-beta precursor protein
J: Amyloid-beta precursor protein


Theoretical massNumber of molelcules
Total (without water)38,11310
Polymers38,11310
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
Amyloid-beta precursor protein


Mass: 3811.330 Da / Num. of mol.: 10 / Mutation: delta(19-24) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: brain / Variant: Tg-UppSwe / Tissue: brain / References: UniProt: Q60495
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: Amyloid fibrils of amyloid-beta(1-42)delta(19-24) extracted from mouse brain.
Type: TISSUE / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse) / Organ: brain / Tissue: brain
Buffer solutionpH: 7
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: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
13PHENIX1.20.1model refinement
14ISOLDE1.7.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 178.4 ° / Axial rise/subunit: 2.36 Å / Axial symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 329437 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0072070
ELECTRON MICROSCOPYf_angle_d0.7992770
ELECTRON MICROSCOPYf_dihedral_angle_d5.902290
ELECTRON MICROSCOPYf_chiral_restr0.064330
ELECTRON MICROSCOPYf_plane_restr0.002340

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