[English] 日本語
Yorodumi
- EMDB-3851: Near-atomic resolution fibril structure of complete amyloid-beta(... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
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

Science, 2017 StrPapers
Fibril structure of amyloid-ß(1-42) by cryoelectron 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: Sep 20, 2017

-
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
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

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

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.935 Å
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)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions216216216
Origin-107-107-107
Limit108108108
Spacing216216216
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
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-107-107-107
NC/NR/NS216216216
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

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more