[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

TitleEvolutionarily conserved short linear motifs drive actin filament binding.
Journal, issue, pagesNat Cell Biol, Vol. 28, Issue 7, Page 1437-1452, Year 2026
Publish dateJul 6, 2026
AuthorsThemistoklis Paraschiakos / Biao Yuan / Michael Hecht-Bucher / Kostiantyn Sopelniak / Pasquale Cervero / Lisa Simon / Ksenija Zonjic / Dominic Eggers / Franziska Selle / Jing Li / Ali Biabani / Stefan Linder / Thomas C Marlovits / Sabine Windhorst /
PubMed AbstractRegulation of the actin cytoskeleton by actin-binding proteins is essential for cellular homeostasis, and the mode of actin binding determines the activity of actin-binding proteins. Here we identify ...Regulation of the actin cytoskeleton by actin-binding proteins is essential for cellular homeostasis, and the mode of actin binding determines the activity of actin-binding proteins. Here we identify a 'short linear actin filament-binding motif' (SFM) based on the cryo-electron microscopy structure of the ITPKA-actin filament complex. Using the computational pipeline SLiMFold, we discovered 103 human proteins containing SFMs with diverse cellular roles. Phylogenetic analysis suggests that SFMs arose de novo and are conserved across eukaryotes, exhibiting actin filament-binding affinities of 2-12 µM. Critical residues mediating binding and modulating affinity were defined, and the cryo-electron microscopy structures of two SFM-actin filament complexes revealed that SFM binding decreases actin-filament stiffness. These findings indicate that SFMs regulate actin-filament conformation and serve as anchoring modules that connect actin dynamics to a broad variety of cellular functions, providing a framework for understanding the actin-associated roles of numerous proteins.
External linksNat Cell Biol / PubMed:42410114 / PubMed Central
MethodsEM (helical sym.)
Resolution2.97 - 3.8 Å
Structure data

18866

8r3h

EMDB-18866, PDB-8r3h:
Phalloidin bound F-actin
Method: EM (helical sym.) / Resolution: 3.13 Å

53133

9qgk

EMDB-53133, PDB-9qgk:
F-actin decorated by ITPKA
Method: EM (helical sym.) / Resolution: 2.97 Å

54871

9sgk

EMDB-54871, PDB-9sgk:
F-actin in complex with USP54 M1 actin binding motif
Method: EM (helical sym.) / Resolution: 3.8 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • gallus (bird)
  • amanita phalloides (death cap)
  • homo sapiens (human)
  • gallus gallus (chicken)
KeywordsCYTOSOLIC PROTEIN / cytoskeleton / actin / STRUCTURAL PROTEIN

+
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