EMDB-28740: Brain-derived 42-residue amyloid-beta fibril type A

Basic information

Entry

Database: EMDB / ID: EMD-28740

• Title: Brain-derived 42-residue amyloid-beta fibril type A

Sample

• Complex: amyloid-b 42 (Ab42) fibril
  • Protein or peptide: Beta-amyloid protein 42Amyloid beta

Function / homology

Function:

regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / positive regulation of amyloid fibril formation / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / cholesterol metabolic process / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / neuron projection maintenance / positive regulation of glycolytic process / extracellular matrix organization / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / learning / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / Post-translational protein phosphorylation / synapse organization / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / neuromuscular junction / visual learning / serine-type endopeptidase inhibitor activity / recycling endosome / cognition / positive regulation of inflammatory response / positive regulation of interleukin-6 production / neuron cellular homeostasis / Golgi lumen / endocytosis / positive regulation of non-canonical NF-kappaB signal transduction / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cellular response to amyloid-beta / positive regulation of DNA-binding transcription factor activity / G2/M transition of mitotic cell cycle / cell-cell junction / synaptic vesicle / positive regulation of tumor necrosis factor production / regulation of translation

Domain/homology:

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. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / 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 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

Component:

Amyloid-beta precursor protein

• Biological species: Homo sapiens (human)
• Method: helical reconstruction / cryo EM / Resolution: 2.83 Å
• Authors: Tycko R / Lee M / Yau Y-M / Louis JM

Funding support

United States, 1 items

Organization	Grant number	Country
Not funded		United States

• Citation: Journal: Proc Natl Acad Sci U S A / Year: 2023; Title: Structures of brain-derived 42-residue amyloid-β fibril polymorphs with unusual molecular conformations and intermolecular interactions.; Authors: Myungwoon Lee / Wai-Ming Yau / John M Louis / Robert Tycko / ; Abstract: Fibrils formed by the 42-residue amyloid-β peptide (Aβ42), a main component of amyloid deposits in Alzheimer's disease (AD), are known to be polymorphic, i.e., to contain multiple possible molecular structures. Previous studies of Aβ42 fibrils, including fibrils prepared entirely in vitro or extracted from brain tissue and using solid-state NMR (ssNMR) or cryogenic electron microscopy (cryo-EM) methods, have found polymorphs with differences in amino acid sidechain orientations, lengths of structurally ordered segments, and contacts between cross-β subunit pairs within a single filament. Despite these differences, Aβ42 molecules adopt a common S-shaped conformation in all previously described high-resolution Aβ42 fibril structures. Here we report two cryo-EM-based structures of Aβ42 fibrils that are qualitatively different, in samples derived from AD brain tissue by seeded growth. In type A fibrils, residues 12 to 42 adopt a ν-shaped conformation, with both intra-subunit and intersubunit hydrophobic contacts to form a compact core. In type B fibrils, residues 2 to 42 adopt an υ-shaped conformation, with only intersubunit contacts and internal pores. Type A and type B fibrils have opposite helical handedness. Cryo-EM density maps and molecular dynamics simulations indicate intersubunit K16-A42 salt bridges in type B fibrils and partially occupied K28-A42 salt bridges in type A fibrils. The coexistence of two predominant polymorphs, with differences in N-terminal dynamics, is supported by ssNMR data, as is faithful propagation of structures from first-generation to second-generation brain-seeded Aβ42 fibril samples. These results demonstrate that Aβ42 fibrils can exhibit a greater range of structural variations than seen in previous studies.

History

Deposition	Oct 31, 2022	-
Header (metadata) release	Mar 22, 2023	-
Map release	Mar 22, 2023	-
Update	Mar 22, 2023	-
Current status	Mar 22, 2023	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_28740.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 0.86 Å

Density

Contour Level	By AUTHOR: 0.009
Minimum - Maximum	-0.037047435 - 0.08876042
Average (Standard dev.)	9.7738e-06 (±0.0015273857)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 500 500 500 Spacing 500 500 500
Cell	A=B=C: 430.0 Å α=β=γ: 90.0 °

Supplemental data

Half map: #1

• File: emd_28740_half_map_1.map

Half map: #2

• File: emd_28740_half_map_2.map

Sample components

Entire : amyloid-b 42 (Ab42) fibril

• Entire: Name: amyloid-b 42 (Ab42) fibril

Components

• Complex: amyloid-b 42 (Ab42) fibril
  • Protein or peptide: Beta-amyloid protein 42Amyloid beta

Supramolecule #1: amyloid-b 42 (Ab42) fibril

• Supramolecule: Name: amyloid-b 42 (Ab42) fibril / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 4514.10 kDa/nm

Macromolecule #1: Beta-amyloid protein 42

• Macromolecule: Name: Beta-amyloid protein 42 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 4.520087 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

Experimental details

Structure determination

• Method: cryo EM
• Processing: helical reconstruction
• Aggregation state: filament

Sample preparation

• Concentration: 0.34 mg/mL
• Buffer: pH: 7.4 / Component - Concentration: 10.0 mM / Component - Name: Sodium Phosphate / Details: 10mM Na-phosphate, 0.1% sodium azide
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK I; Details: Preblot for 12-13 seconds and blot for 2.5-3.0 seconds before plunging.

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 3383 / Average exposure time: 1.65 sec. / Average electron dose: 44.65 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Segment selection: Number selected: 374821 / Software - Name: RELION (ver. 4.0.0)
• Startup model: Type of model: NONE / Details: featureless cylinder
• Final angle assignment: Type: NOT APPLICABLE / Software - Name: RELION (ver. 4.0.0); Details: 2.46 Angstrom helical rise and -179.09 degree helical twist
• Final reconstruction: Applied symmetry - Helical parameters - Δz: 2.46 Å; Applied symmetry - Helical parameters - Δ&Phi: -179.09 °; Applied symmetry - Helical parameters - Axial symmetry: C₁ (asymmetric); Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 68481
• Details: Gatan Imaging Filter (GIF) Quantum LS

Atomic model buiding 1

• Details: Manually generated model was fit into the density using PHENIX and UCSF Chimera. Further refinements were performed using Xplor-NIH.
• Refinement: Protocol: OTHER

Output model

PDB-8ezd:
Brain-derived 42-residue amyloid-beta fibril type A