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- PDB-9vxe: The cryo-EM structure of NapIM_type1 amyloid beta 42 fibril. -

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Basic information

Entry
Database: PDB / ID: 9vxe
TitleThe cryo-EM structure of NapIM_type1 amyloid beta 42 fibril.
ComponentsAmyloid-beta precursor protein
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 / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of Wnt signaling pathway / 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 / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of Wnt signaling pathway / 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 / Lysosome Vesicle Biogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / neuron remodeling / nuclear envelope lumen / dendrite development / regulation of multicellular organism growth / 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 / main axon / intracellular copper ion homeostasis / ECM proteoglycans / Notch signaling pathway / response to insulin-like growth factor stimulus / positive regulation of T cell migration / regulation of presynapse assembly / neuronal dense core vesicle / swimming behavior / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / adult locomotory behavior / positive regulation of mitotic cell cycle / axonogenesis / extracellular matrix organization / cellular response to manganese ion / positive regulation of chemokine production / neuron projection maintenance / clathrin-coated pit / astrocyte activation / Mitochondrial protein degradation / regulation of neuron apoptotic process / ionotropic glutamate receptor signaling pathway / platelet alpha granule lumen / learning / response to interleukin-1 / cellular response to copper ion / positive regulation of glycolytic process / cellular response to cAMP / endosome lumen / trans-Golgi network membrane / positive regulation of interleukin-1 beta production / dendritic shaft / positive regulation of long-term synaptic potentiation / protein serine/threonine kinase binding / locomotory behavior / central nervous system development / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / 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 / response to lead ion / Golgi lumen / positive regulation of JNK cascade / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / neuron projection development / endocytosis / positive regulation of inflammatory response / calcium ion transport / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of translation / regulation of gene expression
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: 3.3 Å
AuthorsZhao, Q.Y. / Cui, B.Y. / Liu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The cryo-EM structure of NapIM_type1 amyloid beta 42 fibril.
Authors: Zhao, Q.Y. / Cui, B.Y. / Liu, C.
History
DepositionJul 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 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

Downloads & links

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Assembly

Deposited unit
R: Amyloid-beta precursor protein
S: Amyloid-beta precursor protein
T: Amyloid-beta precursor protein
U: Amyloid-beta precursor protein
V: Amyloid-beta precursor protein
W: Amyloid-beta precursor protein
X: Amyloid-beta precursor protein
Y: Amyloid-beta precursor protein
Z: Amyloid-beta precursor protein
a: Amyloid-beta precursor protein
b: Amyloid-beta precursor protein
c: Amyloid-beta precursor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,07713
Polymers42,72212
Non-polymers3551
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 precursor protein / APP / ABPP / APPI / Alzheimer disease amyloid A4 protein homolog / Alzheimer disease amyloid ...APP / ABPP / APPI / Alzheimer disease amyloid A4 protein homolog / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta (A4) precursor protein / Amyloid-beta A4 protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 3560.128 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05067
#2: Chemical ChemComp-A1EUE / ~{N},~{N}-dimethyl-6-[(~{E})-2-(1,3,3-trimethylindol-1-ium-2-yl)ethenyl]naphthalen-2-amine


Mass: 355.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27N2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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 beta / Type: TISSUE / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 178.5 ° / Axial rise/subunit: 2.4 Å / Axial symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11491 / Symmetry type: HELICAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0092040
ELECTRON MICROSCOPYf_angle_d0.7172744
ELECTRON MICROSCOPYf_dihedral_angle_d9.7721136
ELECTRON MICROSCOPYf_chiral_restr0.068312
ELECTRON MICROSCOPYf_plane_restr0.002352

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