[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitlePhysical basis of amyloid fibril polymorphism.
Journal, issue, pagesNat Commun, Vol. 9, Issue 1, Page 699, Year 2018
Publish dateFeb 16, 2018
AuthorsWilliam Close / Matthias Neumann / Andreas Schmidt / Manuel Hora / Karthikeyan Annamalai / Matthias Schmidt / Bernd Reif / Volker Schmidt / Nikolaus Grigorieff / Marcus Fändrich /
PubMed AbstractPolymorphism is a key feature of amyloid fibril structures but it remains challenging to explain these variations for a particular sample. Here, we report electron cryomicroscopy-based ...Polymorphism is a key feature of amyloid fibril structures but it remains challenging to explain these variations for a particular sample. Here, we report electron cryomicroscopy-based reconstructions from different fibril morphologies formed by a peptide fragment from an amyloidogenic immunoglobulin light chain. The observed fibril morphologies vary in the number and cross-sectional arrangement of a structurally conserved building block. A comparison with the theoretically possible constellations reveals the experimentally observed spectrum of fibril morphologies to be governed by opposing sets of forces that primarily arise from the β-sheet twist, as well as peptide-peptide interactions within the fibril cross-section. Our results provide a framework for rationalizing and predicting the structure and polymorphism of cross-β fibrils, and suggest that a small number of physical parameters control the observed fibril architectures.
External linksNat Commun / PubMed:29453354 / PubMed Central
MethodsEM (helical sym.)
Resolution8.4 - 20.3 Å
Structure data

EMDB-3986:
Morphology II - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM
Method: EM (helical sym.) / Resolution: 8.4 Å

EMDB-3987:
Morphology III - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM
Method: EM (helical sym.) / Resolution: 9.3 Å

EMDB-3988:
Morphology IV - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM
Method: EM (helical sym.) / Resolution: 9.7 Å

EMDB-3989:
Morphology V - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM
Method: EM (helical sym.) / Resolution: 9.4 Å

EMDB-3990:
Morphology VI - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM
Method: EM (helical sym.) / Resolution: 13.4 Å

EMDB-3991:
Morphology VII - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM
Method: EM (helical sym.) / Resolution: 15.9 Å

EMDB-3992:
Morphology VIII - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM
Method: EM (helical sym.) / Resolution: 18.2 Å

EMDB-3993:
Morphology IX - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM
Method: EM (helical sym.) / Resolution: 20.3 Å

EMDB-3994:
Morphology X - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM
Method: EM (helical sym.) / Resolution: 17.7 Å

Source
  • Homo sapiens (human)

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more