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- EMDB-60210: Cryo-EM structure of the Drosophila INDY (apo-asymmetric, pH 6) -

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Basic information

Entry
Database: EMDB / ID: EMD-60210
TitleCryo-EM structure of the Drosophila INDY (apo-asymmetric, pH 6)
Map data
Sample
  • Complex: citrate transporter INDY in nanodiscs
    • Complex: INDY
      • Protein or peptide: Protein I'm not dead yet
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsINDY / SLC13A5 / citrate transporter / Membrane protein
Function / homology
Function and homology information


regulation of triglyceride storage / Sodium-coupled sulphate, di- and tri-carboxylate transporters / pyruvate transport / succinate transport / citrate transmembrane transporter activity / citrate transport / pyruvate transmembrane transporter activity / succinate transmembrane transporter activity / determination of adult lifespan / transmembrane transport ...regulation of triglyceride storage / Sodium-coupled sulphate, di- and tri-carboxylate transporters / pyruvate transport / succinate transport / citrate transmembrane transporter activity / citrate transport / pyruvate transmembrane transporter activity / succinate transmembrane transporter activity / determination of adult lifespan / transmembrane transport / basolateral plasma membrane / plasma membrane
Similarity search - Function
Sodium/sulphate symporter, conserved site / Sodium:sulfate symporter family signature. / Sodium:sulfate symporter transmembrane region / Solute carrier family 13
Similarity search - Domain/homology
Protein I'm not dead yet
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsKim S / Park JG / Choi SH / Kim JW / Jin MS
Funding support Korea, Republic Of, 4 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019M3E5D6063908 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021M3A9I4022846 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2022R1A2C1091278 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1A6A3A01086747 Korea, Republic Of
CitationJournal: Life Sci Alliance / Year: 2025
Title: Cryo-EM structures reveal the H/citrate symport mechanism of INDY.
Authors: Subin Kim / Jun Gyou Park / Seung Hun Choi / Ji Won Kim / Mi Sun Jin /
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.
History
DepositionMay 17, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60210.png

Downloads & links

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Map

FileDownload / File: emd_60210.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 250 pix.
= 206.625 Å		0.83 Å/pix.
x 250 pix.
= 206.625 Å		0.83 Å/pix.
x 250 pix.
= 206.625 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8265 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0655
Minimum - Maximum-0.17546573 - 0.38439035
Average (Standard dev.)0.0015175355 (±0.01501719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 206.625 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60210_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60210_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : citrate transporter INDY in nanodiscs

EntireName: citrate transporter INDY in nanodiscs
Components
  • Complex: citrate transporter INDY in nanodiscs
    • Complex: INDY
      • Protein or peptide: Protein I'm not dead yet
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: citrate transporter INDY in nanodiscs

SupramoleculeName: citrate transporter INDY in nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #2: INDY

SupramoleculeName: INDY / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Protein I'm not dead yet

MacromoleculeName: Protein I'm not dead yet / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 65.637023 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MATETTKMIY TPPPLDIKME IEIGEQPQPP VKCSNFFANH WKGLVVFLVP LLCLPVMLLN EGAEFRCMYL LLVMAIFWVT EALPLYVTS MIPIVAFPIM GIMSSDQTCR LYFKDTLVMF MGGIMVALAV EYCNLHKRLA LRVIQIVGCS PRRLHFGLIM V TMFLSMWI ...String:
MATETTKMIY TPPPLDIKME IEIGEQPQPP VKCSNFFANH WKGLVVFLVP LLCLPVMLLN EGAEFRCMYL LLVMAIFWVT EALPLYVTS MIPIVAFPIM GIMSSDQTCR LYFKDTLVMF MGGIMVALAV EYCNLHKRLA LRVIQIVGCS PRRLHFGLIM V TMFLSMWI SNAACTAMMC PIIQAVLEEL QAQGVCKINH EPQYQIVGGN KKNNEDEPPY PTKITLCYYL GIAYASSLGG CG TIIGTAT NLTFKGIYEA RFKNSTEQMD FPTFMFYSVP SMLVYTLLTF VFLQWHFMGL WRPKSKEAQE VQRGREGADV AKK VIDQRY KDLGPMSIHE IQVMILFIFM VVMYFTRKPG IFLGWADLLN SKDIRNSMPT IFVVVMCFML PANYAFLRYC TRRG GPVPT GPTPSLITWK FIQTKVPWGL VFLLGGGFAL AEGSKQSGMA KLIGNALIGL KVLPNSVLLL VVILVAVFLT AFSSN VAIA NIIIPVLAEM SLAIEIHPLY LILPAGLACS MAFHLPVSTP PNALVAGYAN IRTKDMAIAG IGPTIITIIT LFVFCQ TWG LVVYPNLNSF PEWAQIYAAA ALGNKTH

UniProtKB: Protein I'm not dead yet

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Macromolecule #2: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 801142
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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