[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

TitleVisualizing dynamic tubulin folding in chaperonin TRiC from nonnative nucleus to final native state.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 7878, Year 2025
Publish dateAug 23, 2025
AuthorsYanyan Zhao / Michael F Schmid / Wah Chiu /
PubMed AbstractThe folding nucleus (FN) initiates and enables an efficient protein folding pathway. Despite its essential role, the FN has long remained cryptic. Here we directly visualize the tubulin FN consisting ...The folding nucleus (FN) initiates and enables an efficient protein folding pathway. Despite its essential role, the FN has long remained cryptic. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with nonnatively folded secondary structure elements of tubulin, stabilizing the nucleus poised for transition into its first native domain tertiary structure. Through progressive folding into the native state, we observe that the unfolded sequence of tubulin undergoes drastic spatial rearrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structure elements first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.
External linksNat Commun / PubMed:40849413 / PubMed Central
MethodsEM (single particle)
Resolution3.7 - 6.5 Å
Structure data

47463

9e2s

EMDB-47463, PDB-9e2s:
Apo TRiC in closed conformation
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-47464: TRiC encapsulating tubulin folding nucleus state.
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-47465: Tubulin intermediate state I in human chaperonin TRiC
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-47466: Tubulin intermediate state II in chaperonin TRiC
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-47467: Tubulin intermediate III in chaperonin TRiC
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-47468: Native Tubulin in human chaperonin TRIC
Method: EM (single particle) / Resolution: 6.5 Å

Chemicals

ChemComp-MG:
Unknown entry

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

ChemComp-AF3:
ALUMINUM FLUORIDE

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
KeywordsCHAPERONE / human chaperonin

+
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