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- PDB-9wmi: PsdAB dimer(LMNG) -

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Basic information

Entry
Database: PDB / ID: 9wmi
TitlePsdAB dimer(LMNG)
Components
  • Lantibiotic ABC transporter ATP-binding protein PsdA
  • Lantibiotic ABC transporter permease PsdB
KeywordsTRANSPORT PROTEIN / ABC transpoter
Function / homologyADENOSINE-5'-DIPHOSPHATE / : / :
Function and homology information
Biological speciesBacillus sp. TSA-4 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHe, Y.T. / Fan, W.J. / Luo, M.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structure of the Nisin resistance pump PsdAB reveals an unusual ABC transporter architecture.
Authors: Yutong He / Wenjie Fan / Jian Shi / Bee Koon Gan / Kai Shao / Fan Zhu / Xuechuan Hong / Min Luo /
Abstract: Bacteria have evolved diverse strategies to resist antimicrobial peptides, among them lipid II-targeting lantibiotics such as nisin. PsdAB, an ABC-type transporter regulated by the PsdRS two- ...Bacteria have evolved diverse strategies to resist antimicrobial peptides, among them lipid II-targeting lantibiotics such as nisin. PsdAB, an ABC-type transporter regulated by the PsdRS two-component system, contributes to nisin resistance, though its structural and mechanistic basis have remained unclear. Here, we report the cryo-EM structure of Bacillus subtilis PsdAB, revealing a dimeric assembly with an unusually large central cavity at the TMD interface. Cross-linking studies confirm the dimeric nature of PsdAB both in vitro and in cells. Functional assays demonstrate that dimer-disrupting mutations compromise nisin resistance, highlighting the importance of dimerization for activity. Compared to canonical ABC transporter types, PsdAB adopts an atypical architecture comprising four NBDs and two TMDs arranged around a central cavity, which may accommodate lipid II. We propose that PsdAB represents a previously unrecognized ABC transporter class. These findings offer new insights into transporter-mediated lantibiotic resistance and suggest a potential mechanism of lipid II shielding.
History
DepositionSep 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lantibiotic ABC transporter ATP-binding protein PsdA
B: Lantibiotic ABC transporter ATP-binding protein PsdA
C: Lantibiotic ABC transporter ATP-binding protein PsdA
D: Lantibiotic ABC transporter ATP-binding protein PsdA
E: Lantibiotic ABC transporter permease PsdB
F: Lantibiotic ABC transporter permease PsdB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,18110
Polymers263,4736
Non-polymers1,7094
Water00
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
Lantibiotic ABC transporter ATP-binding protein PsdA


Mass: 29073.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. TSA-4 (bacteria) / Gene: psdA, yvcR, RUI02_17695
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0AA96UMI8
#2: Protein Lantibiotic ABC transporter permease PsdB


Mass: 73589.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. TSA-4 (bacteria) / Gene: psdB, yvcS, RUI02_17690
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0AA96UNF6
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
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: Hexa complex of PsdA and PsdB. / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Bacillus sp. TSA-4 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
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: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61164 / Symmetry type: POINT
RefinementHighest resolution: 3.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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