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- EMDB-63807: Plant chloroplast dicarboxylate transporter AtDiT2.1 bound with malate -

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Basic information

Entry
Database: EMDB / ID: EMD-63807
TitlePlant chloroplast dicarboxylate transporter AtDiT2.1 bound with malate
Map datamain_map
Sample
  • Complex: Plant chloroplast dicarboxylate transporter AtDiT2.1 bound with malate
    • Protein or peptide: Dicarboxylate transporter 2.1, chloroplastic
  • Ligand: (2S)-2-hydroxybutanedioic acid
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: water
Keywordschloroplast / dicarboxylate transporters / C/N coupling / C4 photosynthesis / TRANSPORT PROTEIN
Function / homology
Function and homology information


oxaloacetate transmembrane transporter activity / oxaloacetate transport / malate transmembrane transport / malate transmembrane transporter activity / ammonia assimilation cycle / chloroplast inner membrane / L-glutamate transmembrane transporter activity / L-glutamate transmembrane transport / chloroplast thylakoid / chloroplast envelope ...oxaloacetate transmembrane transporter activity / oxaloacetate transport / malate transmembrane transport / malate transmembrane transporter activity / ammonia assimilation cycle / chloroplast inner membrane / L-glutamate transmembrane transporter activity / L-glutamate transmembrane transport / chloroplast thylakoid / chloroplast envelope / response to nematode / plastid / chloroplast
Similarity search - Function
Citrate carrier CitT-related / Sodium:sulfate symporter transmembrane region / Solute carrier family 13
Similarity search - Domain/homology
Dicarboxylate transporter 2.1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsYang Z / Zhang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32401000 China
CitationJournal: Plant Cell / Year: 2026
Title: Substrate specificity and transport mechanism of the chloroplast dicarboxylate transporters DiT1 and DiT2.
Authors: Zhao Yang / Xue Zhang / Jingtao Zheng / Shunhao Zhou / Ming-Ju Amy Lyu / Miaolian Ma / Xin-Guang Zhu / Fang Yu / Peng Zhang /
Abstract: Dicarboxylate transporters (DiTs) mediate the exchange of dicarboxylates across the chloroplast inner membrane, playing critical roles in C/N coupling, photorespiration, chloroplast redox ...Dicarboxylate transporters (DiTs) mediate the exchange of dicarboxylates across the chloroplast inner membrane, playing critical roles in C/N coupling, photorespiration, chloroplast redox homeostasis, and C4 photosynthesis. DiT1 and DiT2 are Na⁺-independent exchangers of the solute carrier 13 (SLC13) family, and exhibit overlapping yet distinct substrate specificities: DiT1 transports 2-oxoglutarate, malate, and oxaloacetate, while DiT2 additionally transports glutamate and aspartate. However, the structural determinants of their substrate specificity and transport mechanism remain unclear. Here we determined cryo-electron microscopy structures of Arabidopsis thaliana DiT1 and DiT2.1 bound to diverse substrates in dual conformational states. Structural analyses revealed that AtDiT1 possesses a singular dicarboxylate-binding site that is electrostatically incompatible with amino acid substrates, whereas AtDiT2.1 has two distinct sites to accommodate C4- and C5-dicarboxylates, thus allowing amino acids to bind without electrostatic repulsion. Phylogenetic analysis identified an A226S substitution in the substrate-binding site of DiT1, emerging during evolution in the charophyte ancestor of land plants. This substitution enhances oxaloacetate binding affinity in DiT1, which may have improved adaptation to terrestrial environments. Additionally, two conserved positively charged residues in DiTs functionally mimic Na⁺ used by SLC13 co-transporters, thereby enabling a Na⁺-independent elevator-type transport mechanism. These findings provide critical structural and mechanistic insights into the functional divergence of plant DiTs.
History
DepositionMar 17, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63807.png

Downloads & links

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Map

FileDownload / File: emd_63807.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain_map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 280 pix.
= 260.96 Å		0.93 Å/pix.
x 280 pix.
= 260.96 Å		0.93 Å/pix.
x 280 pix.
= 260.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.8638868 - 4.3601456
Average (Standard dev.)0.0022832195 (±0.10967315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 260.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half B

Fileemd_63807_half_map_1.map
Annotationhalf_B
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half A

Fileemd_63807_half_map_2.map
Annotationhalf_A
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Plant chloroplast dicarboxylate transporter AtDiT2.1 bound with malate

EntireName: Plant chloroplast dicarboxylate transporter AtDiT2.1 bound with malate
Components
  • Complex: Plant chloroplast dicarboxylate transporter AtDiT2.1 bound with malate
    • Protein or peptide: Dicarboxylate transporter 2.1, chloroplastic
  • Ligand: (2S)-2-hydroxybutanedioic acid
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: water

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Supramolecule #1: Plant chloroplast dicarboxylate transporter AtDiT2.1 bound with malate

SupramoleculeName: Plant chloroplast dicarboxylate transporter AtDiT2.1 bound with malate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Dicarboxylate transporter 2.1, chloroplastic

MacromoleculeName: Dicarboxylate transporter 2.1, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 55.765598 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKD YKDDDDKDYK DDDDKLEIAA APQDNAPPPP PPSPSPSPSP QGAKLIPLIL SISVGLILRF AVPVPEGVTP QGWQLLSIF LSTIAGLVLS PLPVGAWAFI GLTASIVTKT LSFSAAFSAF TSEVIWLIVI SFFFARGFVK TGLGDRIATY F VKWLGKST ...String:
MDYKDDDDKD YKDDDDKDYK DDDDKLEIAA APQDNAPPPP PPSPSPSPSP QGAKLIPLIL SISVGLILRF AVPVPEGVTP QGWQLLSIF LSTIAGLVLS PLPVGAWAFI GLTASIVTKT LSFSAAFSAF TSEVIWLIVI SFFFARGFVK TGLGDRIATY F VKWLGKST LGLSYGLTLS EALIAPAMPS TTARAGGIFL PIIKSLSLSA GSKPNDSSSR KLGSYLIQSQ FQCAGNSSAL FL TAAAQNL LCLKLAEELG VVISNPWVSW FKAASLPAII SLLCTPLILY KLYPPETKDT PEAPGIAATK LKQMGPVTKN EWI MVGTML LAVTLWICGE TLGIPSVVAA MIGLSILLVL GVLNWDDCLS EKSAWDTLAW FAVLVGMAGQ LTNLGVVTWM SDCV AKVLQ SLSLSWPAAF GLLQAAYFFI HYLFASQTGH VGALFSAFLA MHIAAGVPGI LAALALAYNT NLFGALTHYS SGQAA VYYG AGYVDLPDVF KIGFVMATIN AIIWGVVGTF WWKFLGLY

UniProtKB: Dicarboxylate transporter 2.1, chloroplastic

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Macromolecule #2: (2S)-2-hydroxybutanedioic acid

MacromoleculeName: (2S)-2-hydroxybutanedioic acid / type: ligand / ID: 2 / Number of copies: 2 / Formula: LMR
Molecular weightTheoretical: 134.087 Da
Chemical component information

ChemComp-LMR:
(2S)-2-hydroxybutanedioic acid

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration30 mg/mL
BufferpH: 7.4 / Details: 20 mM HEPES pH 7.4, 150 mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 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: 1.2 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199851
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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