[English] 日本語
Yorodumi
- EMDB-5132: The reconstructed F120 amyloid fibril represents the structure of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5132
TitleThe reconstructed F120 amyloid fibril represents the structure of a selected subpopulation from the Abeta(1-40) fibril sample with a mean crossover distance of 120 nm. The F140 subpopulation with a mean crossover distance of 140 nm had been studied and deposited previously (EMDB accession no. 5008).
Map dataCross-sectional density slice of the F120 amyloid fibril of 24 Angstrom thickness. F120 corresponds to a subpopulation of the Abeta(1-40) amyloid fibril sample with a mean crossover distance of 120 nm.
Sample
  • Sample: Human Abeta (1-40)
  • Protein or peptide: Abeta
KeywordsAlzheimer's disease / micromechanical properties / electron cryo-microscopy / amyloid fibrils
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 10.1 Å
AuthorsSachse C / Faendrich M / Grigorieff N
CitationJournal: Angew Chem Int Ed Engl / Year: 2010
Title: Nanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy.
Authors: Carsten Sachse / Nikolaus Grigorieff / Marcus Fändrich /
History
DepositionOct 10, 2009-
Header (metadata) releaseOct 12, 2009-
Map releaseOct 12, 2009-
UpdateMar 2, 2016-
Current statusMar 2, 2016Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5132_1.tif

Downloads & links

-
Map

FileDownload / File: emd_5132.map.gz / Format: CCP4 / Size: 306.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCross-sectional density slice of the F120 amyloid fibril of 24 Angstrom thickness. F120 corresponds to a subpopulation of the Abeta(1-40) amyloid fibril sample with a mean crossover distance of 120 nm.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 20 pix.
= 48. Å		2.4 Å/pix.
x 40 pix.
= 240. Å		2.4 Å/pix.
x 100 pix.
= 96. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.4 / Movie #1: 1.4
Minimum - Maximum-1.45155275 - 3.52434707
Average (Standard dev.)0.00000001 (±0.9999938)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions4010020
Spacing1004020
CellA: 96.0 Å / B: 240.00002 Å / C: 48.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z4010020
origin x/y/z0.0000.0000.000
length x/y/z96.000240.00048.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS1004020
D min/max/mean-1.4523.5240.000

-
Supplemental data

-
Sample components

-
Entire : Human Abeta (1-40)

EntireName: Human Abeta (1-40)
Components
  • Sample: Human Abeta (1-40)
  • Protein or peptide: Abeta

-
Supramolecule #1000: Human Abeta (1-40)

SupramoleculeName: Human Abeta (1-40) / type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 1
Molecular weightTheoretical: 4.33 KDa

-
Macromolecule #1: Abeta

MacromoleculeName: Abeta / type: protein_or_peptide / ID: 1 / Name.synonym: Abeta / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8.7 / Details: 50 mM Borate
StainingType: NEGATIVE / Details: Blot for 7 seconds before plunging
GridDetails: Quantifoil 400 mesh 1.3 micrometer holes
VitrificationCryogen name: ETHANE / Chamber temperature: 77.2 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: custom-built plunging apparatus. in coldroom at 277 K.
Method: Blot for 7 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureAverage: 93 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification
DateNov 9, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 62 / Average electron dose: 35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58333 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.9 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

DetailsThe fibrils in the sample were selected based on their uniform width. 2. The F120 subset of limited crossover distances (110-130 nm) was chosen for the reconstruction.
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.1 Å / Resolution method: OTHER / Software - Name: SPIDER
CTF correctionDetails: Each particle CTFTILT
Final angle assignmentDetails: one-degree sampling around helical axis, out-of-plane tilt 16 degree deviation (in 1 degree steps)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more