[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

TitleE2 variants for probing E3 ubiquitin ligase activities.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 123, Issue 1, Page e2524899122, Year 2026
Publish dateJan 6, 2026
AuthorsJiale Du / Gisele A Andree / Daniel Horn-Ghetko / Luca Stier / Jaspal Singh / Sebastian Kostrhon / Leo Kiss / Matthias Mann / Sachdev S Sidhu / Brenda A Schulman /
PubMed AbstractE3 ligases partner with E2 enzymes to regulate vast eukaryotic biology. The hierarchical nature of these pairings, with >600 E3s and ~40 E2s in humans, necessitates that E2s cofunction with numerous ...E3 ligases partner with E2 enzymes to regulate vast eukaryotic biology. The hierarchical nature of these pairings, with >600 E3s and ~40 E2s in humans, necessitates that E2s cofunction with numerous different E3s. Here, focusing on E3s in the RING-between-RING (RBR) family and their partner UBE2L3 and UBE2D-family E2s, we report an approach to interrogate selected pathways. We screened phage-displayed libraries of structure-based E2 variants (E2Vs) to discover enzymes with enhanced affinity and specificity toward half of all RBR E3 ligases (ARIH1, ARIH2, ANKIB1, CUL9, HOIL1, HOIP, and RNF14). Collectively, these E2Vs allowed distinguishing actions of different cofunctioning E3s, obtaining high-resolution cryogenic Electron Microscopy (cryo-EM) structures of an RBR E3 in the context of a substrate-bound multiprotein complex, and profiling an endogenous RBR E3 response to an extracellular stimulus. Overall, we anticipate that E2V technology will be a generalizable tool to enable in-depth mechanistic and structural analysis of E3 ligase functions, and mapping their activity states and protein partners in cellular signaling cascades.
External linksProc Natl Acad Sci U S A / PubMed:41481455 / PubMed Central
MethodsEM (single particle)
Resolution2.83 - 3.23 Å
Structure data

54793

9sdx

EMDB-54793: Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2~L3A2-1~Ub
PDB-9sdx: Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub
Method: EM (single particle) / Resolution: 2.97 Å

54794

9sdy

EMDB-54794, PDB-9sdy:
Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2
Method: EM (single particle) / Resolution: 3.06 Å

EMDB-54795: Cryo-EM map of focus refined ASB9-Elob/C-CKB bound to Nedd8-CUL5-RBX2-ARIH2-L3A2-1
Method: EM (single particle) / Resolution: 2.83 Å

EMDB-54892: consensus map of Neddylated CUL5-ARIH2-L3A2-1 bound to ASB9-EloB/C-CKB
Method: EM (single particle) / Resolution: 3.06 Å

EMDB-54893: Focus refined map of Neddylated CUL5-ARIH2-L3A2-1 bound to ASB9-EloB/C-CKB, focus refined on ARIH2-L3A2-1
Method: EM (single particle) / Resolution: 3.23 Å

EMDB-54933: Consensus Map of Neddylated CUL5 C-terminal region-RBX2-ARIH2~L3A2-1~Ub
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-54934: Focus refined map of Neddylated CUL5 C-terminal region-RBX2-ARIH2~L3A2-1~Ub
Method: EM (single particle) / Resolution: 3.17 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SY8:
5-azanylpentan-2-one

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsLIGASE / Complex

+
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