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- PDB-9mct: Plant chloroplast dicarboxylate transporter AtDiT1 bound with 2-OG -

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Entry
Database: PDB / ID: 9mct
TitlePlant chloroplast dicarboxylate transporter AtDiT1 bound with 2-OG
ComponentsDicarboxylate transporter 1, chloroplastic
KeywordsTRANSPORT PROTEIN / chloroplast / dicarboxylate transporters / C/N coupling / C4 photosynthesis
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 / alpha-ketoglutarate transport / alpha-ketoglutarate transmembrane transporter activity / chloroplast thylakoid / chloroplast envelope ...oxaloacetate transmembrane transporter activity / oxaloacetate transport / malate transmembrane transport / malate transmembrane transporter activity / ammonia assimilation cycle / chloroplast inner membrane / alpha-ketoglutarate transport / alpha-ketoglutarate transmembrane transporter activity / 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
2-OXOGLUTARIC ACID / Dicarboxylate transporter 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsYang, Z. / Zhang, P.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Dicarboxylate transporter 1, chloroplastic
B: Dicarboxylate transporter 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8254
Polymers110,5332
Non-polymers2922
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Dicarboxylate transporter 1, chloroplastic / 2-oxoglutarate/malate translocator 1 / AtpOMT1


Mass: 55266.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DIT1, At5g12860, T24H18.30 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9LXV3
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Plant chloroplast dicarboxylate transporter AtDiT1 bound with 2-OG
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4 / Details: 20 mM HEPES pH 7.4, 150 mM NaCl
SpecimenConc.: 30 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.14_3260: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92146 / Symmetry type: POINT

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