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- EMDB-2433: Amyloid-beta nanotube -

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Basic information

Entry
Database: EMDB / ID: EMD-2433
TitleAmyloid-beta nanotube
Map dataReconstruction of an amyloid-beta nanotube
Sample
  • Sample: Amyloid-Beta (1-42) nanotube
  • Protein or peptide: Amyloid-beta (1-42)
Keywordsnanotube / neurodegeneration / prion-dependent synaptotoxicity
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining
AuthorsNicoll AJ / Panico S / Freir DB / Wright D / Terry C / Risse E / Herron CE / O'Malley T / Wadsworth JD / Farrow MA ...Nicoll AJ / Panico S / Freir DB / Wright D / Terry C / Risse E / Herron CE / O'Malley T / Wadsworth JD / Farrow MA / Walsh DM / Saibil HR / Collinge J
CitationJournal: Nat Commun / Year: 2013
Title: Amyloid-β nanotubes are associated with prion protein-dependent synaptotoxicity.
Authors: Andrew J Nicoll / Silvia Panico / Darragh B Freir / Daniel Wright / Cassandra Terry / Emmanuel Risse / Caroline E Herron / Tiernan O'Malley / Jonathan D F Wadsworth / Mark A Farrow / Dominic ...Authors: Andrew J Nicoll / Silvia Panico / Darragh B Freir / Daniel Wright / Cassandra Terry / Emmanuel Risse / Caroline E Herron / Tiernan O'Malley / Jonathan D F Wadsworth / Mark A Farrow / Dominic M Walsh / Helen R Saibil / John Collinge /
Abstract: Growing evidence suggests water-soluble, non-fibrillar forms of amyloid-β protein (Aβ) have important roles in Alzheimer's disease with toxicities mimicked by synthetic Aβ(1-42). However, no ...Growing evidence suggests water-soluble, non-fibrillar forms of amyloid-β protein (Aβ) have important roles in Alzheimer's disease with toxicities mimicked by synthetic Aβ(1-42). However, no defined toxic structures acting via specific receptors have been identified and roles of proposed receptors, such as prion protein (PrP), remain controversial. Here we quantify binding to PrP of Aβ(1-42) after different durations of aggregation. We show PrP-binding and PrP-dependent inhibition of long-term potentiation (LTP) correlate with the presence of protofibrils. Globular oligomers bind less avidly to PrP and do not inhibit LTP, whereas fibrils inhibit LTP in a PrP-independent manner. That only certain transient Aβ assemblies cause PrP-dependent toxicity explains conflicting reports regarding the involvement of PrP in Aβ-induced impairments. We show that these protofibrils contain a defined nanotubular structure with a previously unidentified triple helical conformation. Blocking the formation of Aβ nanotubes or their interaction with PrP might have a role in treatment of Alzheimer's disease.
History
DepositionJul 29, 2013-
Header (metadata) releaseAug 7, 2013-
Map releaseSep 18, 2013-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

image2433.png

Downloads & links

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Map

FileDownload / File: emd_2433.map.gz / Format: CCP4 / Size: 459 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of an amyloid-beta nanotube
Voxel sizeX=Y=Z: 3.26 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.01752149 - 0.05421662
Average (Standard dev.)0.00494013 (±0.01042412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions494950
Spacing494950
CellA: 159.74 Å / B: 159.74 Å / C: 163.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.263.263.26
M x/y/z494950
origin x/y/z0.0000.0000.000
length x/y/z159.740159.740163.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS494950
D min/max/mean-0.0180.0540.005

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Supplemental data

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Sample components

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Entire : Amyloid-Beta (1-42) nanotube

EntireName: Amyloid-Beta (1-42) nanotube
Components
  • Sample: Amyloid-Beta (1-42) nanotube
  • Protein or peptide: Amyloid-beta (1-42)

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Supramolecule #1000: Amyloid-Beta (1-42) nanotube

SupramoleculeName: Amyloid-Beta (1-42) nanotube / type: sample / ID: 1000
Details: Protofibrils were prepared from synthetic Amyloid-Beta (1-42) peptide. Briefly hexafluoro-2-propanol-trated Amyloid-beta (1-42) was dissolved in DMSO, diluted into phenol red-free Hams-F12 ...Details: Protofibrils were prepared from synthetic Amyloid-Beta (1-42) peptide. Briefly hexafluoro-2-propanol-trated Amyloid-beta (1-42) was dissolved in DMSO, diluted into phenol red-free Hams-F12 medium, centrifuged and incubated at 22 C for 16 hours. Size of protofibrils ranged from 0.1 to 1 megadaltons
Oligomeric state: protofibrils / Number unique components: 1
Molecular weightExperimental: 500 KDa
Method: size-exclusion chromatography with static light scattering

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Macromolecule #1: Amyloid-beta (1-42)

MacromoleculeName: Amyloid-beta (1-42) / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.1 mg/mL
BufferDetails: phenol red-free Ham's F12 cell medium (2% DMSO)
StainingType: NEGATIVE
Details: Grids with adsorbed protein were stained with 2% w/v uranyl acetate for 1 minute
GridDetails: Negatively glow discharged 300 mesh copper grid with continuous carbon layer
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 42986 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 42000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Alignment procedureLegacy - Astigmatism: corrected for at specimen level
DateJan 10, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 50 / Average electron dose: 20 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: phase flipping, whole micrograph
Final two d classificationNumber classes: 6
Final reconstructionApplied symmetry - Helical parameters - Δz: 3.26 Å
Applied symmetry - Helical parameters - Δ&Phi: 15 °
Algorithm: OTHER / Software - Name: Spider
Details: Maps were calculated from individual classes. Final volume is the average of six maps (maps averaged in CHIMERA). Helical pitch repeat was obtained from tomography data. Since the subunit ...Details: Maps were calculated from individual classes. Final volume is the average of six maps (maps averaged in CHIMERA). Helical pitch repeat was obtained from tomography data. Since the subunit repeat could not be determined, continuous helices were generated.
Number images used: 155
DetailsThree-dimensional reconstructions were calculated from extracted, aligned and classified segments and applying helical symmetry, using the pitch independently determined from tomography and single pixel increments in z to generate continuous helices.

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