8ZL1 | pdb_00008zl1

Cryo-EM structure of the Drosophila INDY (apo outward-open, pH 6)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures reveal the H + /citrate symport mechanism of Drosophila INDY.

Kim, S.Park, J.G.Choi, S.H.Kim, J.W.Jin, M.S.

(2025) Life Sci Alliance 8

  • DOI: https://doi.org/10.26508/lsa.202402992
  • Primary Citation of Related Structures:  
    8ZKW, 8ZKZ, 8ZL1, 8ZL2, 8ZL3, 8ZL4, 8ZL6

  • PubMed Abstract: 

    Drosophila 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.


  • Organizational Affiliation
    • School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein I'm not dead yet
A, B
590Drosophila melanogasterMutation(s): 0 
Gene Names: IndyCG3979
Membrane Entity: Yes 
UniProt
Find proteins for Q9VVT2 (Drosophila melanogaster)
Explore Q9VVT2 
Go to UniProtKB:  Q9VVT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VVT2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2019M3E5D6063908
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021M3A9I4022846
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2022R1A2C1091278
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021R1A6A3A01086747

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Data collection
  • Version 1.2: 2025-08-13
    Changes: Data collection, Database references