EMDB-21501: Amyloid-beta(1-40) fibril derived from Alzheimer's disease cortic...

Basic information

• Entry: Database: EMDB / ID: EMD-21501
• Title: Amyloid-beta(1-40) fibril derived from Alzheimer's disease cortical tissue
• Sample: amyloid-beta(1-40) fibrils derived from human AD brain:; Amyloid-beta precursor protein

Function / homology

Function:

amylin binding / acetylcholine receptor activator activity / positive regulation of protein import / regulation of acetylcholine-gated cation channel activity / positive regulation of G protein-coupled receptor internalization / positive regulation of cellular response to thapsigargin / positive regulation of cellular response to tunicamycin / amyloid-beta complex / regulation of response to calcium ion / signaling receptor activator activity / positive regulation of response to endoplasmic reticulum stress / growth cone lamellipodium / positive regulation of 1-phosphatidylinositol-3-kinase activity / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / endosome to plasma membrane transport vesicle / microglia development / regulation of epidermal growth factor-activated receptor activity / regulation of dendritic spine maintenance / protein trimerization / positive regulation of endothelin production / negative regulation of blood circulation / mating behavior / lipoprotein particle / regulation of amyloid-beta clearance / positive regulation of oxidative stress-induced neuron death / smooth endoplasmic reticulum calcium ion homeostasis / negative regulation of mitochondrion organization / regulation of amyloid fibril formation / regulation of spontaneous synaptic transmission / tumor necrosis factor production / axon midline choice point recognition / synaptic growth at neuromuscular junction / astrocyte activation involved in immune response / cellular process / regulation of synapse structure or activity / positive regulation of amyloid fibril formation / modulation of excitatory postsynaptic potential / PTB domain binding / intermediate-density lipoprotein particle / astrocyte projection / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / Golgi-associated vesicle / ciliary rootlet / peptidase activator activity / positive regulation of G protein-coupled receptor signaling pathway / axo-dendritic transport / activation of MAPKKK activity / positive regulation of protein metabolic process / positive regulation of cell activation / main axon / RAGE receptor binding / neuron remodeling / negative regulation of protein localization to nucleus / high-density lipoprotein particle / positive regulation of T cell migration / frizzled binding / response to yeast / heparan sulfate binding / heparan sulfate proteoglycan binding / lipoprotein metabolic process / dendrite development / COPII-coated ER to Golgi transport vesicle / nuclear envelope lumen / suckling behavior / regulation of presynapse assembly / positive regulation of membrane protein ectodomain proteolysis / positive regulation of chemokine production => GO:0032722 / positive regulation of protein kinase A signaling / negative regulation of pri-miRNA transcription by RNA polymerase II / mRNA polyadenylation / positive regulation of monocyte chemotaxis / smooth endoplasmic reticulum / acetylcholine receptor binding / low-density lipoprotein particle receptor binding / antifungal humoral response / negative regulation of long-term synaptic potentiation / cellular copper ion homeostasis / growth factor receptor binding / neuromuscular process controlling balance / positive regulation of tumor necrosis factor production => GO:0032760 / apolipoprotein binding / positive regulation of amyloid-beta formation / negative regulation of neuron differentiation / transition metal ion binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / regulation of toll-like receptor signaling pathway / associative learning / trans-Golgi network membrane / regulation of NMDA receptor activity / positive regulation of tau-protein kinase activity / positive regulation of excitatory postsynaptic potential / regulation of Wnt signaling pathway / RNA polymerase II core promoter sequence-specific DNA binding / spindle midzone / clathrin-coated pit / chemoattractant activity / regulation of peptidyl-tyrosine phosphorylation / synapse organization

Domain/homology:

Amyloidogenic glycoprotein, copper-binding domain superfamily / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Beta-amyloid precursor protein C-terminal / Pancreatic trypsin inhibitor Kunitz domain superfamily / Amyloid-beta precursor protein / Amyloidogenic glycoprotein / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Amyloidogenic glycoprotein, E2 domain / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, copper-binding / Proteinase inhibitor I2, Kunitz, conserved site / PH-like domain superfamily / Amyloidogenic glycoprotein, intracellular domain, conserved site / Amyloidogenic glycoprotein, copper-binding domain conserved site / Pancreatic trypsin inhibitor Kunitz domain / Amyloidogenic glycoprotein, amyloid-beta peptide

Component:

Amyloid-beta precursor protein

• Biological species: Homo sapiens (human)
• Method: helical reconstruction / cryo EM / Resolution: 2.77 Å
• Authors: Ghosh U / Thurber KR / Tycko R
• Citation: Journal: Proc Natl Acad Sci U S A / Year: 2021; Title: Molecular structure of a prevalent amyloid-β fibril polymorph from Alzheimer's disease brain tissue.; Authors: Ujjayini Ghosh / Kent R Thurber / Wai-Ming Yau / Robert Tycko / ; Abstract: Amyloid-β (Aβ) fibrils exhibit self-propagating, molecular-level polymorphisms that may contribute to variations in clinical and pathological characteristics of Alzheimer's disease (AD). We report the molecular structure of a specific fibril polymorph, formed by 40-residue Aβ peptides (Aβ40), that is derived from cortical tissue of an AD patient by seeded fibril growth. The structure is determined from cryogenic electron microscopy (cryoEM) images, supplemented by mass-per-length (MPL) measurements and solid-state NMR (ssNMR) data. Previous ssNMR studies with multiple AD patients had identified this polymorph as the most prevalent brain-derived Aβ40 fibril polymorph from typical AD patients. The structure, which has 2.8-Å resolution according to standard criteria, differs qualitatively from all previously described Aβ fibril structures, both in its molecular conformations and its organization of cross-β subunits. Unique features include twofold screw symmetry about the fibril growth axis, despite an MPL value that indicates three Aβ40 molecules per 4.8-Å β-sheet spacing, a four-layered architecture, and fully extended conformations for molecules in the central two cross-β layers. The cryoEM density, ssNMR data, and MPL data are consistent with β-hairpin conformations for molecules in the outer cross-β layers. Knowledge of this brain-derived fibril structure may contribute to the development of structure-specific amyloid imaging agents and aggregation inhibitors with greater diagnostic and therapeutic utility.
• Validation Report: Summary, Full report, XML, About validation report

History

Deposition	Mar 2, 2020	-
Header (metadata) release	Apr 1, 2020	-
Map release	Jan 13, 2021	-
Update	Jan 27, 2021	-
Current status	Jan 27, 2021	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_21501.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.08 Å

Density

Contour Level	By AUTHOR: 0.021 / Movie #1: 0.021
Minimum - Maximum	-0.0682921 - 0.13522795
Average (Standard dev.)	-3.7405164e-06 (±0.0031375533)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 432.00003 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.08	1.08	1.08
M x/y/z	400	400	400
origin x/y/z	0.000	0.000	0.000
length x/y/z	432.000	432.000	432.000
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	400	400	400
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	400	400	400
D min/max/mean	-0.068	0.135	-0.000

Supplemental data

Segmentation: #1

• File: emd_21501_msk_1.map

Sample components

Entire amyloid-beta(1-40) fibrils derived from human AD brain

• Entire: Name: amyloid-beta(1-40) fibrils derived from human AD brain; Details: Fibrils produced by seeded growth using amyloid-beta in brain extract as the source of seeds. CryoEM and solid state NMR measurements were performed on second-generation seeded fibrils.; Number of components: 2

Component #1: protein, amyloid-beta(1-40) fibrils derived from human AD brain

• Protein: Name: amyloid-beta(1-40) fibrils derived from human AD brain; Details: Fibrils produced by seeded growth using amyloid-beta in brain extract as the source of seeds. CryoEM and solid state NMR measurements were performed on second-generation seeded fibrils.; Recombinant expression: No
• Mass: Experimental: 29 MDa
• Source: Species: Homo sapiens (human)

Component #2: protein, Amyloid-beta precursor protein

• Protein: Name: Amyloid-beta precursor protein / Number of Copies: 6 / Recombinant expression: No
• Mass: Theoretical: 4.335852 kDa
• Source: Species: Homo sapiens (human)

Experimental details

Sample preparation

• Specimen: Specimen state: Filament / Method: cryo EM
• Helical parameters: Axial symmetry: C₁ (asymmetric) / Delta z: 2.45 Å / Delta phi: 179.66 %deg
• Sample solution: Specimen conc.: 0.45 mg/mL; Buffer solution: 10 mM phosphate buffer with 0.01% NaN3 to avoid microbial contamination. Buffers were filtered to avoid contamination.; pH: 7.4
• Support film: The grids were checked in microscope prior to use.
• Vitrification: Instrument: LEICA PLUNGER / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 90 %; Details: The grids were preblotted for 10 seconds and blotted for 6 seconds before plunging..

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Imaging: Microscope: TFS KRIOS; Details: Preliminary grid screening was done manually in FEI T12.
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 73.5 e/Ų / Illumination mode: FLOOD BEAM
• Lens: Magnification: 130000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -500.0 - -3000.0 nm / Energy filter: GIF Quantum LS
• Specimen Holder: Model: FEI TITAN KRIOS AUTOGRID HOLDER
• Camera: Detector: GATAN K2 QUANTUM (4k x 4k)

Image acquisition

• Image acquisition: Number of digital images: 1337

Image processing

• Processing: Method: helical reconstruction; Details: The selected images were corrected for gain. The gain reference was not rotated or flipped.
• 3D reconstruction: Algorithm: FOURIER SPACE / Software: RELION; CTF correction: The correction was done in Gctf and is corrected for amplitude. Per -particle CTF refinement was done prior to final reconstruction.; Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF; Details: A modified version of RELION 3.0-beta was used for the reconstruction. The modified version allowed local averaging of the rotation angle. Final reconstruction used 2-fold screw symmetry.

Atomic model buiding

• Modeling #1: Refinement space: REAL; Details: Xplor-NIH was used to combine EM density with phi/psi restraints from NMR chemical shifts (from Talos-N Version 4.21 Rev 2016.343.11.31).

Output model

6w0o