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- EMDB-5052: cryoEM structure of Abeta(1-42) amyloid fibrils -

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Basic information

Entry
Database: EMDB / ID: EMD-5052
TitlecryoEM structure of Abeta(1-42) amyloid fibrils
Map dataThis is a cryoEM map of a segment of Abeta(1-42) amyloid fibrils.
Sample
  • Sample: Abeta(1-42) amyloid fibril
  • Protein or peptide: Abeta(1-42) amyloid fibril
KeywordsAlzheimer's disease / amyloid fibrils / Abeta(1-42) / neurodegenerative disease / IHRSR
Methodhelical reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsZhang R / Hu X / Khant H / Ludtke SJ / Chiu W / Schmid MF / Frieden C / Lee J-M
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: Interprotofilament interactions between Alzheimer's Abeta1-42 peptides in amyloid fibrils revealed by cryoEM.
Authors: Rui Zhang / Xiaoyan Hu / Htet Khant / Steven J Ludtke / Wah Chiu / Michael F Schmid / Carl Frieden / Jin-Moo Lee /
Abstract: Alzheimer's disease is a neurodegenerative disorder characterized by the accumulation of amyloid plaques in the brain. This amyloid primarily contains amyloid-beta (Abeta), a 39- to 43-aa peptide ...Alzheimer's disease is a neurodegenerative disorder characterized by the accumulation of amyloid plaques in the brain. This amyloid primarily contains amyloid-beta (Abeta), a 39- to 43-aa peptide derived from the proteolytic cleavage of the endogenous amyloid precursor protein. The 42-residue-length Abeta peptide (Abeta(1-42)), the most abundant Abeta peptide found in plaques, has a much greater propensity to self-aggregate into fibrils than the other peptides and is believed to be more pathogenic. Synthetic human Abeta(1-42) peptides self-aggregate into stable but poorly-ordered helical filaments. We determined their structure to approximately 10-A resolution by using cryoEM and the iterative real-space reconstruction method. This structure reveals 2 protofilaments winding around a hollow core. Previous hairpin-like NMR models for Abeta(17-42) fit well in the cryoEM density map and reveal that the juxtaposed protofilaments are joined via the N terminus of the peptide from 1 protofilament connecting to the loop region of the peptide in the opposite protofilament. This model of mature Abeta(1-42) fibrils is markedly different from previous cryoEM models of Abeta(1-40) fibrils. In our model, the C terminus of Abeta forms the inside wall of the hollow core, which is supported by partial proteolysis analysis.
History
DepositionFeb 15, 2009-
Header (metadata) releaseMar 9, 2009-
Map releaseJul 7, 2010-
UpdateMar 2, 2016-
Current statusMar 2, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.98
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.98
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5052_1.png

Downloads & links

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Map

FileDownload / File: emd_5052.map.gz / Format: CCP4 / Size: 89 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cryoEM map of a segment of Abeta(1-42) amyloid fibrils.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.81 Å/pix.
x 288 pix.
= 521.28 Å		1.81 Å/pix.
x 288 pix.
= 521.28 Å		1.81 Å/pix.
x 288 pix.
= 521.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.98 / Movie #1: 0.98
Minimum - Maximum-0.75612682 - 1.78369975
Average (Standard dev.)0.00254699 (±0.12236803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-144-144-144
Dimensions288288288
Spacing288288288
CellA=B=C: 521.27997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.811.811.81
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z521.280521.280521.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-144-144-144
NC/NR/NS288288288
D min/max/mean-0.7561.7840.003

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Supplemental data

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Sample components

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Entire : Abeta(1-42) amyloid fibril

EntireName: Abeta(1-42) amyloid fibril
Components
  • Sample: Abeta(1-42) amyloid fibril
  • Protein or peptide: Abeta(1-42) amyloid fibril

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Supramolecule #1000: Abeta(1-42) amyloid fibril

SupramoleculeName: Abeta(1-42) amyloid fibril / type: sample / ID: 1000
Details: The sample was prepared in 10mM HCl buffer for 1 month to form fibrils.
Number unique components: 1

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Macromolecule #1: Abeta(1-42) amyloid fibril

MacromoleculeName: Abeta(1-42) amyloid fibril / type: protein_or_peptide / ID: 1 / Name.synonym: Abeta(1-42) amyloid fibril
Details: The component of this amyloid fibril is a 42-residue peptide. Dry synthetic human Abeta1-42 peptides were purchased from American Peptide Company Inc.
Oligomeric state: helical / Recombinant expression: No / Database: NCBI
Molecular weightExperimental: 5 KDa / Theoretical: 5 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 2 / Details: 10mM HCl, 2% DMSO
GridDetails: Quantifoil 200 mesh grid
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 90 K / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: 2 blots, each 2 seconds before plunging

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 93 K / Max: 93 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 400,000 times magnification
Specialist opticsEnergy filter - Name: JEOL
DateDec 9, 2006
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Number real images: 208 / Average electron dose: 18 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe long straight filaments were boxed out from the raw electron micrograph using EMAN helixboxer program.
Final reconstructionApplied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IHRSR
Details: We sorted heterogeneous dataset into homogeneous subgroups. And the deposited map is the reconstruction for one of the subgroups .
CTF correctionDetails: each micrograph by binnary phase flipping

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Atomic model buiding 1

Initial modelPDB ID:

2beg


Chain - Chain ID: A
DetailsPDBEntryID_givenInChain. Protocol: manually fit. manually fit 10 abeta(1-42) monomers into one strand of cryoEM map.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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