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- PDB-21fi: Cryo-EM structure of DddT in closed DMSP-bound conformation -

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Entry
Database: PDB / ID: 21fi
TitleCryo-EM structure of DddT in closed DMSP-bound conformation
ComponentsDddT
KeywordsTRANSPORT PROTEIN / Trimer / Psychrobacter sp. D2 / Dimethylsulfoniopropionate transporter / Closed DMSP-bound conformation
Function / homology3-(dimethyl-lambda~4~-sulfanyl)propanoic acid
Function and homology information
Biological speciesPsychrobacter sp. D2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsZhu, W.J. / Wang, P.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 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
D: DddT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0924
Polymers54,9091
Non-polymers1823
Water543
1
D: DddT
hetero molecules

D: DddT
hetero molecules

D: DddT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,27512
Polymers164,7283
Non-polymers5479
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

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Components

#1: Protein DddT


Mass: 54909.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter sp. D2 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-DQY / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid


Mass: 136.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: DddT in closed DMSP-bound conformation / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Psychrobacter sp. D2 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 446735 / Symmetry type: POINT
RefinementHighest resolution: 2.52 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044000
ELECTRON MICROSCOPYf_angle_d0.6335454
ELECTRON MICROSCOPYf_dihedral_angle_d4.693530
ELECTRON MICROSCOPYf_chiral_restr0.079638
ELECTRON MICROSCOPYf_plane_restr0.006653

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