[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

TitleA trimeric architecture reveals the glucitol PTS transporter as a distinct superfamily.
Journal, issue, pagesCommun Biol, Vol. 9, Issue 1, Year 2026
Publish dateMar 10, 2026
AuthorsTingyue Deng / Xueli Liu / Jianwei Zeng / Xiaofei Ge / Jiawei Wang /
PubMed AbstractThe bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS) catalyzes the transport and phosphorylation of carbohydrates. The glucitol (Gut) PTS transporter from Escherichia coli has ...The bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS) catalyzes the transport and phosphorylation of carbohydrates. The glucitol (Gut) PTS transporter from Escherichia coli has often been discussed in relation to the Glucose-Fructose-Lactose (GFL) superfamily, although other work has suggested that it may instead form a separate PTS superfamily. This uncertainty is linked to its unusual genetic organization, in which the transmembrane IIC domain is divided into two polypeptides (IIC1/GutE and IIC2/GutA). Here, we present the cryo-electron microscopy (cryo-EM) structure of the complete Gut transporter, which resolves this discrepancy by revealing a homotrimeric architecture for its transmembrane domain-a fold unprecedented among sugar-transporting PTS permeases. This structural evidence supports the view that the Gut family represents a distinct PTS superfamily. Within the trimer, the protomers are captured in inward-facing and inward-occluded conformations, providing a structural basis for an alternating-access transport mechanism. Furthermore, the structure suggests a unique in-trans phosphotransfer pathway between the IIB and IIC domains of adjacent subunits and identifies the substrate-binding pocket at the GutA/GutE interface. Our work redefines the structural landscape of PTS transporters and provides a mechanistic framework for sugar transport by this unique trimeric porter.
External linksCommun Biol / PubMed:41807737 / PubMed Central
MethodsEM (single particle)
Resolution3.44 Å
Structure data

66479

9x2m

EMDB-66479, PDB-9x2m:
Gut transporter with sorbitol
Method: EM (single particle) / Resolution: 3.44 Å

Chemicals

ChemComp-SOR:
sorbitol

Source
  • Escherichia coli (E. coli)
  • escherichia coli k-12 (bacteria)
KeywordsTRANSPORT PROTEIN / sugar phosphotransferase system / PTS / glucitol/sorbitol / PTS Gut family

+
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