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- EMDB-3851: Near-atomic resolution fibril structure of complete amyloid-beta(... -

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Basic information

Database: EMDB / ID: 3851
TitleNear-atomic resolution fibril structure of complete amyloid-beta(1-42) by cryo-EM
SampleBeta-amyloid protein 42 fibrils
SourceHomo sapiens / human
Map dataThe density map was sharpened by a B-factor of -50 Ang^2 and filtered to 3.5 Ang. This density map was used for model building and refinement.
Methodhelical reconstruction, at 4 Å resolution
AuthorsGremer L / Schoelzel D
CitationScience, 2017, 358, 116-119

Science, 2017, 358, 116-119 Yorodumi Papers
Fibril structure of amyloid-β(1-42) by cryo-electron microscopy.
Lothar Gremer / Daniel Schölzel / Carla Schenk / Elke Reinartz / Jörg Labahn / Raimond B G Ravelli / Markus Tusche / Carmen Lopez-Iglesias / Wolfgang Hoyer / Henrike Heise / Dieter Willbold / Gunnar F Schröder

Validation ReportPDB-ID: 5oqv

SummaryFull reportAbout validation report
DateDeposition: Aug 14, 2017 / Header (metadata) release: Sep 13, 2017 / Map release: Sep 13, 2017 / Last update: Oct 18, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5oqv
  • Surface level: 0.028
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5oqv
  • Imaged by Jmol
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3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_3851.map.gz (map file in CCP4 format, 40311 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
216 pix
0.94 Å/pix.
= 201.96 Å
216 pix
0.94 Å/pix.
= 201.96 Å
216 pix
0.94 Å/pix.
= 201.96 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.935 Å
Contour Level:0.028 (by author), 0.028 (movie #1):
Minimum - Maximum-0.2759506 - 0.35235986
Average (Standard dev.)3.571115E-5 (0.012035223)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 201.96 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9350.9350.935
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z201.960201.960201.960
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-50-50-50
D min/max/mean-0.2760.3520.000

Supplemental data

Sample components

Entire Beta-amyloid protein 42 fibrils

EntireName: Beta-amyloid protein 42 fibrils / Number of components: 2

Component #1: protein, Beta-amyloid protein 42 fibrils

ProteinName: Beta-amyloid protein 42 fibrils / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

Component #2: protein, Amyloid beta A4 protein

ProteinName: Amyloid beta A4 protein / Recombinant expression: No
MassTheoretical: 4.520087 kDa
Source (engineered)Expression System: Homo sapiens / human

Experimental details

Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 2.335 Å / Delta phi: -179.275 deg.
Sample solutionBuffer solution: in water / pH: 2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: 2.5 microL sample was applied to the grid, blotted for 2.5 s before plunging.

Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 24 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 110000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

Image acquisition

Image acquisitionNumber of digital images: 2026

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: SPARX / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
Details: For the even/odd test, the fibrils were split after the final reconstruction (no gold-standard). These two half sets were then refined further independently for another 12 iterations.
FSC plot (resolution assessment)

Atomic model buiding

Output model

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