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- PDB-9umh: V-type (V2-type) amyloid fibril (40) of Tottori (D7N) mutant -

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Basic information

Entry
Database: PDB / ID: 9umh
TitleV-type (V2-type) amyloid fibril (40) of Tottori (D7N) mutant
ComponentsAmyloid-beta protein 40
KeywordsPROTEIN FIBRIL / Amyloid
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / regulation of synapse structure or activity / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / Golgi-associated vesicle / PTB domain binding / astrocyte projection / neuron remodeling / Lysosome Vesicle Biogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / dendrite development / regulation of multicellular organism growth / nuclear envelope lumen / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / transition metal ion binding / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / modulation of excitatory postsynaptic potential / intracellular copper ion homeostasis / Notch signaling pathway / main axon / ECM proteoglycans / response to insulin-like growth factor stimulus / positive regulation of T cell migration / regulation of presynapse assembly / neuronal dense core vesicle / swimming behavior / adult locomotory behavior / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of calcium-mediated signaling / extracellular matrix organization / positive regulation of mitotic cell cycle / axonogenesis / cellular response to manganese ion / neuron projection maintenance / clathrin-coated pit / astrocyte activation / regulation of neuron apoptotic process / Mitochondrial protein degradation / positive regulation of glycolytic process / ionotropic glutamate receptor signaling pathway / platelet alpha granule lumen / learning / response to interleukin-1 / cellular response to cAMP / cellular response to copper ion / endosome lumen / trans-Golgi network membrane / locomotory behavior / positive regulation of interleukin-1 beta production / dendritic shaft / central nervous system development / positive regulation of long-term synaptic potentiation / protein serine/threonine kinase binding / Post-translational protein phosphorylation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / microglial cell activation / cellular response to nerve growth factor stimulus / visual learning / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / synapse organization / positive regulation of interleukin-6 production / recycling endosome / positive regulation of JNK cascade / response to lead ion / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / endocytosis / neuron projection development / positive regulation of inflammatory response / calcium ion transport / positive regulation of tumor necrosis factor production / regulation of translation / regulation of gene expression / Platelet degranulation / 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 speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBurton-Smith, R.N. / Murata, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP24ama121005 Japan
CitationJournal: ACS Chem Neurosci / Year: 2025
Title: Microgravity-Assisted Exploration of the Conformational Space of Amyloid β Affected by Tottori-Type Familial Mutation D7N.
Authors: Maho Yagi-Utsumi / Saeko Yanaka / Raymond N Burton-Smith / Chihong Song / Christian Ganser / Chiaki Yamazaki / Haruo Kasahara / Toru Shimazu / Takayuki Uchihashi / Kazuyoshi Murata / Koichi Kato /
Abstract: The amyloid β (Aβ) Tottori variant (D7N) exhibits unique aggregation behaviors and altered fibril formation, posing challenges for structural characterization. To overcome this, the microgravity ...The amyloid β (Aβ) Tottori variant (D7N) exhibits unique aggregation behaviors and altered fibril formation, posing challenges for structural characterization. To overcome this, the microgravity environment on the International Space Station was employed to study Tottori-type Aβ40 fibril formation and structure. Under Earth gravity, Tottori-type Aβ40 primarily formed nonfibrillar aggregates, hindering detailed structural analysis. In contrast, microgravity significantly enhanced fibril formation and minimized amorphous aggregates. Cryo-electron microscopy revealed two structurally distinct fibril types, each comprising different protomer conformations. In both types, the N-terminal segment was disordered and nor resolved in the density maps. The D7N mutation disrupts the protection of the core by the N-terminal segment often observed in wild-type Aβ40 fibrils, enhancing the hydrophobicity-mediated aggregation propensity. However, microgravity suppressed kinetic traps and facilitated high-quality fibril formation suitable for structural studies that can explore the free energy landscape of Aβ fibril formation. These findings demonstrate the utility of microgravity for studying familial Aβ variants and potentially accelerate our understanding of Aβ aggregation mechanisms in Alzheimer's disease.
History
DepositionApr 22, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AL: Amyloid-beta protein 40
AM: Amyloid-beta protein 40
AN: Amyloid-beta protein 40
AO: Amyloid-beta protein 40
AP: Amyloid-beta protein 40
AQ: Amyloid-beta protein 40
AR: Amyloid-beta protein 40
AS: Amyloid-beta protein 40
AT: Amyloid-beta protein 40
AU: Amyloid-beta protein 40
AV: Amyloid-beta protein 40
AW: Amyloid-beta protein 40
AX: Amyloid-beta protein 40
AY: Amyloid-beta protein 40
AZ: Amyloid-beta protein 40
Aa: Amyloid-beta protein 40
Ab: Amyloid-beta protein 40
Ac: Amyloid-beta protein 40
Ad: Amyloid-beta protein 40
Ae: Amyloid-beta protein 40
Af: Amyloid-beta protein 40


Theoretical massNumber of molelcules
Total (without water)91,03221
Polymers91,03221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
Amyloid-beta protein 40 / Abeta40 / Beta-APP40


Mass: 4334.867 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05067
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: V-shaped amyloid beta fibre (type 1) (Tottori mutant - D7N)
Type: COMPLEX / 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 1400 nm / Nominal defocus min: 800 nm / Cs: 0.021 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: 179.149 ° / Axial rise/subunit: 2.415 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218123 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.003442210.0119
ELECTRON MICROSCOPYs_angle_nonh_deg0.771256281.7701
ELECTRON MICROSCOPYs_dihedral_angle_1_deg7.3725465
ELECTRON MICROSCOPYs_dihedral_angle_2_deg0.1452425
ELECTRON MICROSCOPYs_dihedral_angle_3_deg9.1431119710
ELECTRON MICROSCOPYs_dihedral_angle_6_deg10.865127310
ELECTRON MICROSCOPYs_chiral_restr0.02466300.1302
ELECTRON MICROSCOPYs_planes0.00257960.02
ELECTRON MICROSCOPYs_nbd0.201746090.2
ELECTRON MICROSCOPYs_nbtor0.200475050.2
ELECTRON MICROSCOPYs_hbond_nbd0.1059980.2

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