[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

TitleCryo-EM structures reveal the H/citrate symport mechanism of INDY.
Journal, issue, pagesLife Sci Alliance, Vol. 8, Issue 4, Year 2025
Publish dateJan 30, 2025
AuthorsSubin Kim / Jun Gyou Park / Seung Hun Choi / Ji Won Kim / Mi Sun Jin /
PubMed Abstract I'm Not Dead Yet (INDY) functions as a transporter for citrate, a key metabolite in the citric acid cycle, across the plasma membrane. Partial deficiency of INDY extends lifespan, akin to the ... I'm Not Dead Yet (INDY) functions as a transporter for citrate, a key metabolite in the citric acid cycle, across the plasma membrane. Partial deficiency of INDY extends lifespan, akin to the effects of caloric restriction. In this work, we use cryo-electron microscopy to determine structures of INDY in the presence and absence of citrate and in complex with the well-known inhibitor 4,4'-diisothiocyano-2,2'-disulfonic acid stilbene (DIDS) at resolutions ranging from 2.7 to 3.6 Å. Together with functional data obtained in vitro, the INDY structures reveal the H/citrate co-transport mechanism, in which aromatic residue F119 serves as a one-gate element. They also provide insight into how protein-lipid interactions at the dimerization interface affect the stability and function of the transporter, and how DIDS disrupts the transport cycle.
External linksLife Sci Alliance / PubMed:39884835 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.65 Å
Structure data

60210

8zkw

EMDB-60210, PDB-8zkw:
Cryo-EM structure of the Drosophila INDY (apo-asymmetric, pH 6)
Method: EM (single particle) / Resolution: 2.77 Å

60213

8zkz

EMDB-60213, PDB-8zkz:
Cryo-EM structure of the Drosophila INDY (apo-asymmetric, pH8)
Method: EM (single particle) / Resolution: 2.7 Å

60215

8zl1

EMDB-60215, PDB-8zl1:
Cryo-EM structure of the Drosophila INDY (apo outward-open, pH 6)
Method: EM (single particle) / Resolution: 2.86 Å

60216

8zl2

EMDB-60216, PDB-8zl2:
Cryo-EM structure of the Drosophila INDY (DIDS-bound asymmetric, pH 6)
Method: EM (single particle) / Resolution: 2.8 Å

60217

8zl3

EMDB-60217, PDB-8zl3:
Cryo-EM structure of the Drosophila INDY (DIDS-bound outward-open, pH 6)
Method: EM (single particle) / Resolution: 2.9 Å

60218

8zl4

EMDB-60218, PDB-8zl4:
Cryo-EM structure of the Drosophila INDY (citrate-bound inward-occluded, pH 6)
Method: EM (single particle) / Resolution: 3.65 Å

60220

8zl6

EMDB-60220: Cryo-EM structure of the Drosophila INDY (apo inward-open, pH8)
PDB-8zl6: Cryo-EM structure of the Drosophila INDY (apo inward-open, pH 8)
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-4DS:
4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid / inhibitor*YM

ChemComp-FLC:
CITRATE ANION

Source
  • drosophila melanogaster (fruit fly)
KeywordsMEMBRANE PROTEIN / INDY / SLC13A5 / citrate transporter / DIDS / citrate

+
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