[English] 日本語
Yorodumi
- EMDB-60216: Cryo-EM structure of the Drosophila INDY (DIDS-bound asymmetric, pH 6) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60216
TitleCryo-EM structure of the Drosophila INDY (DIDS-bound asymmetric, pH 6)
Map data
Sample
  • Complex: citrate transporter INDY in nanodiscs
    • Complex: INDY
      • Protein or peptide: Protein I'm not dead yet
  • Ligand: 4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsINDY / SLC13A5 / citrate transporter / Membrane protein / DIDS
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: 2.8 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: To Be Published
Title: Cryo-EM structures reveal the cation-independent citrate transport mechanism of the Drosophila longevity protein, INDY
Authors: Kim S / Park JG / Choi SH / Kim JW / Jin MS
History
DepositionMay 17, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60216.png

Downloads & links

-
Map

FileDownload / File: emd_60216.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.)
0.85 Å/pix.
x 250 pix.
= 212.81 Å		0.85 Å/pix.
x 250 pix.
= 212.81 Å		0.85 Å/pix.
x 250 pix.
= 212.81 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85124 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.15337732 - 0.39322278
Average (Standard dev.)0.0027145057 (±0.017841658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 212.80951 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60216_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60216_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: 4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
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)

-
Supramolecule #2: INDY

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

-
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

-
Macromolecule #2: 4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid

MacromoleculeName: 4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid / type: ligand / ID: 2 / Number of copies: 1 / Formula: 4DS
Molecular weightTheoretical: 454.52 Da
Chemical component information

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

-
Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

-
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: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 483241
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more