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- EMDB-67626: Cryo-EM structure of DddT in closed DMSP-bound conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-67626
TitleCryo-EM structure of DddT in closed DMSP-bound conformation
Map data
Sample
  • Complex: DddT in closed DMSP-bound conformation
    • Protein or peptide: DddT
  • Ligand: 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsTrimer / Psychrobacter sp. D2 / Dimethylsulfoniopropionate transporter / Closed DMSP-bound conformation / TRANSPORT PROTEIN
Biological speciesPsychrobacter sp. D2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 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_67626.png

Downloads & links

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Map

FileDownload / File: emd_67626.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 300 pix.
= 291. Å		0.97 Å/pix.
x 300 pix.
= 291. Å		0.97 Å/pix.
x 300 pix.
= 291. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.0547428 - 3.1226816
Average (Standard dev.)0.0024678807 (±0.06480003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 291.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67626_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67626_half_map_2.map
Projections & Slices
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Sample components

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Entire : DddT in closed DMSP-bound conformation

EntireName: DddT in closed DMSP-bound conformation
Components
  • Complex: DddT in closed DMSP-bound conformation
    • Protein or peptide: DddT
  • Ligand: 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: DddT in closed DMSP-bound conformation

SupramoleculeName: DddT in closed DMSP-bound conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 54.909449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NKIDWFIFIS TFVLIVAICL PLVLYPEKGG ELVSQANSFV TSNFGMVFLW AGMGGFAFLT YLFFSEHGKI KFGTKDEKPE FSNFSWGAM VFCAGVASGL VYWGTIEWAY YFTAPPYGIE PKSTDAAEIA AAYGIFHWGP SAWAFFVLPS LPIAYSYYIL K VPVLRLSE ...String:
NKIDWFIFIS TFVLIVAICL PLVLYPEKGG ELVSQANSFV TSNFGMVFLW AGMGGFAFLT YLFFSEHGKI KFGTKDEKPE FSNFSWGAM VFCAGVASGL VYWGTIEWAY YFTAPPYGIE PKSTDAAEIA AAYGIFHWGP SAWAFFVLPS LPIAYSYYIL K VPVLRLSE ICRIVIGKHS DGVLGKVIDI IFMFGILGAA GTSLGLGTPL VAAGISKITG IESSTSMTVF VLVLCTALFT WS AYSGLKR GLKLLSDLAI ICSVILLTYV LLVGPTEFIL KMGTNSVGLL FTNFVRWNLY TDPVSGSGFV ESWTVFYWAW WIV YTPFMG LFIAKISRGR TIRQVILGGI AWGTLGCAAY FSILGNYAMH LELTKELSVT GLLEQIGAPA TIMEVIGTLP LGSV VVIVF SFIALIFLAT TFDSAAYMMA SSTTPTLGLN EEPAKWNRLF WALTLFILPG TLMVLGGDLK TLQTASILTA IPFIF VIML LVVALMKMLK TGEHFNQD

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Macromolecule #2: 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid

MacromoleculeName: 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid / type: ligand / ID: 2 / Number of copies: 1 / Formula: DQY
Molecular weightTheoretical: 136.213 Da
Chemical component information

ChemComp-DQY:
3-(dimethyl-lambda~4~-sulfanyl)propanoic acid

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 3 / 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

BufferpH: 8
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: 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: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 446735
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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