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- PDB-9pym: Cryo-EM structure of the isethionate TRAP transporter IseQM from ... -

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Basic information

Entry
Database: PDB / ID: 9pym
TitleCryo-EM structure of the isethionate TRAP transporter IseQM from Oleidesulfovibrio alaskensis with bound isethionate
Components
  • Isethionate TRAP transporter permease protein DctMQ
  • Megabody C7HopQ
KeywordsTRANSPORT PROTEIN / TRAP Transporter / Megabody / Isethionate
Function / homology
Function and homology information


alkanesulfonate catabolic process / transmembrane transporter activity / plasma membrane
Similarity search - Function
TRAP transporter large membrane protein DctM / TRAP C4-dicarboxylate transport system permease DctM subunit / : / Tripartite ATP-independent periplasmic transporters, DctQ component / Tripartite ATP-independent periplasmic transporter, DctM component
Similarity search - Domain/homology
2-hydroxyethylsulfonic acid / PHOSPHATIDYLETHANOLAMINE / Isethionate TRAP transporter permease protein DctMQ
Similarity search - Component
Biological speciesOleidesulfovibrio alaskensis G20 (bacteria)
Helicobacter pylori (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsNewton-Vesty, M.C. / Davies, J.S. / Dobson, R.C.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: Structure / Year: 2025
Title: Structural basis of isethionate transport by a TRAP transporter from a sulfate-reducing bacterium.
Authors: Michael C Newton-Vesty / Mariafrancesca Scalise / Sam A Jamieson / Michael J Currie / Hamish G Brown / Sepideh Valimehr / Zachary D Tillett / Kelsi R Hall / Senwei Quan / Jane R Allison / ...Authors: Michael C Newton-Vesty / Mariafrancesca Scalise / Sam A Jamieson / Michael J Currie / Hamish G Brown / Sepideh Valimehr / Zachary D Tillett / Kelsi R Hall / Senwei Quan / Jane R Allison / Andrew E Whitten / Santosh Panjikar / Cesare Indiveri / Eric Hanssen / Peter D Mace / Rachel A North / Renwick C J Dobson / James S Davies /
Abstract: Sulfate-reducing bacteria import organosulfur compounds from the environment for anaerobic respiration. They contribute to human disease and are problematic in industrial settings because they ...Sulfate-reducing bacteria import organosulfur compounds from the environment for anaerobic respiration. They contribute to human disease and are problematic in industrial settings because they produce hydrogen sulfide. Here, we demonstrate how the sulfate-reducing bacterium Oleidesulfovibrio alaskensis imports isethionate, a common organosulfonate, using a tripartite ATP-independent periplasmic (TRAP) transporter (OaIsePQM). The cryo-EM structure of isethionate-bound OaIseQM to 2.98 Å resolution defines the substrate-binding site, two Na-binding sites, and a distinct fusion helix. Key residues within the OaIseQM substrate-binding site are identified using substitution and proteoliposome assays. Functional studies demonstrate that OaIseQM requires the substrate-binding protein (OaIseP) and a Na gradient to drive transport. Modeling of the OaIsePQM complex supports that elevator-type conformational changes are involved in this unique coupled transport process. This work expands our knowledge of the transport of organosulfur compounds in bacteria and establishes OaIsePQM as a new model system for exploring the mechanism of TRAP transporters.
History
DepositionAug 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isethionate TRAP transporter permease protein DctMQ
B: Megabody C7HopQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4087
Polymers123,0562
Non-polymers2,3515
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Isethionate TRAP transporter permease protein DctMQ / TRAP transporter / fused DctMQ subunit


Mass: 67592.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oleidesulfovibrio alaskensis G20 (bacteria)
Gene: dctMQ, Dde_1274 / Production host: Escherichia coli (E. coli) / References: UniProt: Q312S1
#2: Antibody Megabody C7HopQ


Mass: 55463.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-8X3 / 2-hydroxyethylsulfonic acid / 2-oxidanylethanesulfonic acid


Mass: 126.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

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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: IseQM complexed with Megabody C7HopQ / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Oleidesulfovibrio alaskensis G20 (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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 66 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83854 / Symmetry type: POINT

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