[English] 日本語
Yorodumi
- EMDB-5008: Paired beta-sheet structure of an Abeta(1-40) amyloid fibril reve... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5008
TitlePaired beta-sheet structure of an Abeta(1-40) amyloid fibril revealed by electron microscopy
Map dataThe volume contains a total of 10 asymmetric units of the fibril
Sample
  • Sample: human Abeta(1-40)
  • Protein or peptide: AbetaAmyloid beta
KeywordsAlzheimers disease / amyloid-beta / electron cryo-microscopy / protein folding / neurodegeneration
Function / homologyAmyloidogenic glycoprotein, amyloid-beta peptide
Function and homology information
Methodhelical reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsSachse C / Faendrich M / Grigorieff N
CitationJournal: Proc Natl Acad Sci U S A / Year: 2008
Title: Paired beta-sheet structure of an Abeta(1-40) amyloid fibril revealed by electron microscopy.
Authors: Carsten Sachse / Marcus Fändrich / Nikolaus Grigorieff /
Abstract: Alzheimer's disease is a neurodegenerative disorder that is characterized by the cerebral deposition of amyloid fibrils formed by Abeta peptide. Despite their prevalence in Alzheimer's and other ...Alzheimer's disease is a neurodegenerative disorder that is characterized by the cerebral deposition of amyloid fibrils formed by Abeta peptide. Despite their prevalence in Alzheimer's and other neurodegenerative diseases, important details of the structure of amyloid fibrils remain unknown. Here, we present a three-dimensional structure of a mature amyloid fibril formed by Abeta(1-40) peptide, determined by electron cryomicroscopy at approximately 8-A resolution. The fibril consists of two protofilaments, each containing approximately 5-nm-long regions of beta-sheet structure. A local twofold symmetry within each region suggests that pairs of beta-sheets are formed from equivalent parts of two Abeta(1-40) peptides contained in each protofilament. The pairing occurs via tightly packed interfaces, reminiscent of recently reported steric zipper structures. However, unlike these previous structures, the beta-sheet pairing is observed within an amyloid fibril and includes significantly longer amino acid sequences.
History
DepositionMar 7, 2008-
Header (metadata) releaseMar 25, 2008-
Map releaseOct 8, 2009-
UpdateOct 14, 2009-
Current statusOct 14, 2009Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_5008.map.gz / Format: CCP4 / Size: 2.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe volume contains a total of 10 asymmetric units of the fibril
Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy EMDB: 1.25 / Movie #1: 1.2
Minimum - Maximum-1.3446 - 3.68503
Average (Standard dev.)-0.000000000894781 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions7520040
Spacing7520040
CellA: 90 Å / B: 240 Å / C: 48 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z7520040
origin x/y/z0.0000.0000.000
length x/y/z90.000240.00048.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS2007540
D min/max/mean-1.3453.685-0.000

-
Supplemental data

-
Sample components

-
Entire : human Abeta(1-40)

EntireName: human Abeta(1-40)
Components
  • Sample: human Abeta(1-40)
  • Protein or peptide: AbetaAmyloid beta

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

SupramoleculeName: human Abeta(1-40) / type: sample / ID: 1000 / 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
SequenceInterPro: Amyloidogenic glycoprotein, amyloid-beta peptide

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.8 / Details: 50 mM Borate
GridDetails: Quantifoil R1.2/1.3 Cu 400 mesh grids
VitrificationCryogen name: ETHANE / Chamber temperature: 77.2 K / Instrument: OTHER / Details: Vitrification carried out in cold room at 277 K. / Method: Blot for 7 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58333 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 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
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 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each particle CTFTILT
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 1 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details1. The fibrils in the sample were selected based on their uniform width. 2. A subset of limited crossover distances (130-150 nm) was chosen for the reconstruction.

+
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