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Near-atomic resolution fibril structure of complete amyloid-beta(1-42) by cryo-EM

by helical reconstruction, at 4 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.028, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.028, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 3851
TitleNear-atomic resolution fibril structure of complete amyloid-beta(1-42) by cryo-EM
MapThe 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.
SampleBeta-amyloid protein 42 fibrils
AuthorsGremer L, Schoelzel D
DateDeposition: 2017-08-14, Header release: 2017-09-13, Map release: 2017-09-13, Last update: 2017-09-13
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.028, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.028, Imaged by UCSF CHIMERA

Supplemental images
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Related Structure Data
Related Entries

PDB-5oqv

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Fit: output model of fitting

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Article
Citation - Primary
ArticleScience, Year 2017
TitleFibril structure of amyloid-ß(1-42) by cryoelectron microscopy.
AuthorsLothar 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
Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
Centre for Structural Systems Biology (CSSB), DESY, 22607 Hamburg, Germany.
The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, Netherlands.
Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
LinksPubMed: 28882996, DOI: 10.1126/science.aao2825
Map
Fileemd_3851.map.gz ( map file in CCP4 format, 40311 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
216 pix
0.935 A/pix
= 201.96 A
216 pix
0.935 A/pix
= 201.96 A
216 pix
0.935 A/pix
= 201.96 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.028 (by author), 0.028 (movie #1):
Minimum - Maximum: -0.2759506 - 0.35235986
Average (Standard dev.): 3.571115E-5 (0.012035223)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions216216216
Origin-107-107-107
Limit108108108
Spacing216216216
Unit CellA= B= C: 201.96 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 0.935 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-107-107-107
NC/NR/NS216216216
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.2760.3520.000
Annotation DetailsThe 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.
Supplement
Images
Images
FSC
FSC
Sample
NameBeta-amyloid protein 42 fibrils
Number of Components2
Component #1: protein - Beta-amyloid protein 42 fibrils
Scientific nameBeta-amyloid protein 42 fibrils
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #2: protein - Amyloid beta A4 protein
Scientific nameAmyloid beta A4 protein
Theoretical Mass0.004520087 MDa
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 9606
Expression system: Homo sapiens
Experiment
Sample Preparation
Specimen Statefilament
BufferpH: 2
Details: in water
Helical ParametersDelta Phi: -179.275 degrees
Delta Z: 2.335 A
Axial Symmetry: C1
Vitrification
Cryogen NameETHANE
InstrumentFEI VITROBOT MARK IV
Details2.5 microL sample was applied to the grid, blotted for 2.5 s before plunging.
Imaging
MicroscopeFEI TECNAI ARCTICA
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose24 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 110000
Nominal Cs2.7 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelOTHER
Camera
DetectorOTHER
Image Acquisition
#1
Number of Digital Images2026
Processing
Methodhelical reconstruction
3D reconstruction
SoftwareSPARX
Resolution By Author
4 A
Resolution MethodFSC 0.143 CUT-OFF
DetailsFor 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.
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-3851-v19.xml (6.5 KB)
emd-3851-v20.xml (15.3 KB)
emd-3851.xml (6.5 KB)
Map dataemd_3851.map.gz (36.1 MB)
Imagesemd_3851.png (147.8 KB)
FSC (resolution estimation)emd_3851_fsc.xml (7.7 KB)
Othersemd_3851_half_map_1.map.gz (13.5 MB)
emd_3851_half_map_2.map.gz (13.5 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-3851
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 7 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 7.2 MB
Session file for UCSF-Chimera, 27 KB