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- EMDB-67627: Cryo-EM structure of DddT in closed substrate-free conformation i... -

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Entry
Database: EMDB / ID: EMD-67627
TitleCryo-EM structure of DddT in closed substrate-free conformation in the presence of potassium ions and dimethylsulfoniopropionate
Map data
Sample
  • Complex: DddT in closed substrate-free conformation in the presence of potassium ions and dimethylsulfoniopropionate
    • Protein or peptide: DddT
KeywordsTrimer / Psychrobacter sp. D2 / Dimethylsulfoniopropionate transporter / Closed substrate-free conformation in the presence of potassium ions and dimethylsulfoniopropionate / TRANSPORT PROTEIN
Biological speciesPsychrobacter sp. D2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsZhu WJ / Wang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32170127 China
CitationJournal: EMBO J / Year: 2026
Title: Structural insights into bacterial dimethylsulfoniopropionate import by BCCT-family transporters.
Authors: Yu-Zhong Zhang / Wen-Jing Zhu / Kang Li / Hai-Tao Ding / Motoyuki Hattori / Shuaimeng Liu / Chang Ge / Qi-Long Qin / Zhao-Jie Teng / Ning-Hua Liu / Hai-Yan Cao / Chun-Yang Li / Xiu-Lan Chen ...Authors: Yu-Zhong Zhang / Wen-Jing Zhu / Kang Li / Hai-Tao Ding / Motoyuki Hattori / Shuaimeng Liu / Chang Ge / Qi-Long Qin / Zhao-Jie Teng / Ning-Hua Liu / Hai-Yan Cao / Chun-Yang Li / Xiu-Lan Chen / Qing-Tao Shen / Jonathan D Todd / Lu-Ning Liu / Peng Wang /
Abstract: Dimethylsulfoniopropionate (DMSP) is a ubiquitous marine organosulfur compound central to microbial stress responses, chemotaxis, and nutrient cycling. Its catabolism produces dimethylsulfide (DMS), ...Dimethylsulfoniopropionate (DMSP) is a ubiquitous marine organosulfur compound central to microbial stress responses, chemotaxis, and nutrient cycling. Its catabolism produces dimethylsulfide (DMS), a climate-active gas, and plays a key role in the global sulfur cycle. However, the molecular basis of DMSP import, underpinning its microbial metabolism, remains poorly understood. Here, we identify and characterize the BCCT-family transporter DddT from Psychrobacter sp. D2, a marine gamma-proteobacterium that utilizes DMSP as a carbon source. DddT is essential for DMSP uptake and functions as a Na-coupled symporter driven by the transmembrane sodium gradient. Using cryo-electron microscopy, we determined DddT structures in multiple conformational states, revealing its Na-dependent transport mechanism involving two sodium ions, one coordinated by a previously uncharacterized binding site. Sequence analysis shows that DddT-like proteins with conserved sodium-binding features are widespread in marine bacteria, suggesting this Na-coupled transport mechanism represents a broadly conserved feature of the BCCT family. Our findings provide mechanistic insights into sodium-driven substrate uptake and marine sulfur cycling.
History
DepositionDec 11, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67627.png

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Map

FileDownload / File: emd_67627.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 192 pix.
= 248.319 Å		1.29 Å/pix.
x 192 pix.
= 248.319 Å		1.29 Å/pix.
x 192 pix.
= 248.319 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.29333 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.244
Minimum - Maximum-2.7969859 - 4.29307
Average (Standard dev.)0.012946303 (±0.087390244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 248.31935 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67627_half_map_1.map
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Half map: #1

Fileemd_67627_half_map_2.map
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Sample components

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Entire : DddT in closed substrate-free conformation in the presence of pot...

EntireName: DddT in closed substrate-free conformation in the presence of potassium ions and dimethylsulfoniopropionate
Components
  • Complex: DddT in closed substrate-free conformation in the presence of potassium ions and dimethylsulfoniopropionate
    • Protein or peptide: DddT

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Supramolecule #1: DddT in closed substrate-free conformation in the presence of pot...

SupramoleculeName: DddT in closed substrate-free conformation in the presence of potassium ions and dimethylsulfoniopropionate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Psychrobacter sp. D2 (bacteria)

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Macromolecule #1: DddT

MacromoleculeName: DddT / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Psychrobacter sp. D2 (bacteria)
Molecular weightTheoretical: 57.731621 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LKENKIDWFI FISTFVLIVA ICLPLVLYPE KGGELVSQAN SFVTSNFGMV FLWAGMGGFA FLTYLFFSEH GKIKFGTKDE KPEFSNFSW GAMVFCAGVA SGLVYWGTIE WAYYFTAPPY GIEPKSTDAA EIAAAYGIFH WGPSAWAFFV LPSLPIAYSY Y ILKVPVLR ...String:
LKENKIDWFI FISTFVLIVA ICLPLVLYPE KGGELVSQAN SFVTSNFGMV FLWAGMGGFA FLTYLFFSEH GKIKFGTKDE KPEFSNFSW GAMVFCAGVA SGLVYWGTIE WAYYFTAPPY GIEPKSTDAA EIAAAYGIFH WGPSAWAFFV LPSLPIAYSY Y ILKVPVLR LSEICRIVIG KHSDGVLGKV IDIIFMFGIL GAAGTSLGLG TPLVAAGISK ITGIESSTSM TVFVLVLCTA LF TWSAYSG LKRGLKLLSD LAIICSVILL TYVLLVGPTE FILKMGTNSV GLLFTNFVRW NLYTDPVSGS GFVESWTVFY WAW WIVYTP FMGLFIAKIS RGRTIRQVIL GGIAWGTLGC AAYFSILGNY AMHLELTKEL SVTGLLEQIG APATIMEVIG TLPL GSVVV IVFSFIALIF LATTFDSAAY MMASSTTPTL GLNEEPAKWN RLFWALTLFI LPGTLMVLGG DLKTLQTASI LTAIP FIFV IMLLVVALMK MLKTGEHFNQ DLQDDPIKLA EVDSLEERQK PAA

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2wsw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 373892
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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