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- EMDB-64138: PsdAB dimer (peptidisc sample) -

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Basic information

Entry
Database: EMDB / ID: EMD-64138
TitlePsdAB dimer (peptidisc sample)
Map data
Sample
  • Complex: Hexa complex of PsdA and PsdB.
    • Protein or peptide: Lantibiotic ABC transporter ATP-binding protein PsdA
    • Protein or peptide: Lantibiotic ABC transporter permease PsdB
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsABC transpoter / TRANSPORT PROTEIN
Function / homology: / :
Function and homology information
Biological speciesBacillus sp. TSA-4 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHe YT / Fan WJ / Shao K / Luo M
Funding support Singapore, 1 items
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
DepositionApr 11, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64138.png

Downloads & links

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Map

FileDownload / File: emd_64138.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.37636662 - 0.78338873
Average (Standard dev.)0.002824799 (±0.031747118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64138_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64138_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexa complex of PsdA and PsdB.

EntireName: Hexa complex of PsdA and PsdB.
Components
  • Complex: Hexa complex of PsdA and PsdB.
    • Protein or peptide: Lantibiotic ABC transporter ATP-binding protein PsdA
    • Protein or peptide: Lantibiotic ABC transporter permease PsdB
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Hexa complex of PsdA and PsdB.

SupramoleculeName: Hexa complex of PsdA and PsdB. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus sp. TSA-4 (bacteria)

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Macromolecule #1: Lantibiotic ABC transporter ATP-binding protein PsdA

MacromoleculeName: Lantibiotic ABC transporter ATP-binding protein PsdA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. TSA-4 (bacteria)
Molecular weightTheoretical: 29.073227 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MNVLQTTNLS KTYYSNKGTI SYQALSAFDL SVSKGEFVGI MGPSGSGKTT LLNLLATIDK PTQGEMMING IQPKTLKDQE LALFRRREL GFVFQDFNLL DTLTIRENIL LPLALDKVKL REMEARLDEL ADTLQIKHIL DHRTYEVSGG QQQRAACARA I IHNPALIL ...String:
MNVLQTTNLS KTYYSNKGTI SYQALSAFDL SVSKGEFVGI MGPSGSGKTT LLNLLATIDK PTQGEMMING IQPKTLKDQE LALFRRREL GFVFQDFNLL DTLTIRENIL LPLALDKVKL REMEARLDEL ADTLQIKHIL DHRTYEVSGG QQQRAACARA I IHNPALIL ADEPTGNLDS KSAKQVMNTL AQLNEEKEAT ILLVTHDATA ASFCKRIVFI KDGRFFSEIH RGTNRQVFYQ SI LDTLSVL GGDFHEFENY RP

UniProtKB: UNIPROTKB: A0AA96UMI8

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Macromolecule #2: Lantibiotic ABC transporter permease PsdB

MacromoleculeName: Lantibiotic ABC transporter permease PsdB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. TSA-4 (bacteria)
Molecular weightTheoretical: 73.589867 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MNLRTIARKN ILGNLQRYVA YFLSCVFAVS VFFVFTSFIF HPDVNEDNIY GGSLVKTCLS AALVVIIVFC IFFITYSNSA FLQARKKEF GLLTLFGTSK QQLRKMIYYE QSLISLAAIA AGIGAGLLFS KLFFMIMTWM LSVKVPISFA IVPKAFVMTI A GFLILFQT ...String:
MNLRTIARKN ILGNLQRYVA YFLSCVFAVS VFFVFTSFIF HPDVNEDNIY GGSLVKTCLS AALVVIIVFC IFFITYSNSA FLQARKKEF GLLTLFGTSK QQLRKMIYYE QSLISLAAIA AGIGAGLLFS KLFFMIMTWM LSVKVPISFA IVPKAFVMTI A GFLILFQT LLILSLGRIR KLEIIELIKS AKKPKSLPVY SKWLTVLSLL CLGSGYYLSA TANAIDMMFR VFPILILVLV GT YFFFTQS SVAFFRMLYR KKHSFYKGTN IIVRSNMIFR LKDHARMLFL TSVITAVILT ATGVIYMFYS DLQRQEEQSI PQS VSWVEK DASRFQVMKP ETAENTLKKA HAVIKYKVDA TGIPVTFQSD LPYGNKKMEA EALLISEKVY NQVAKEKGFP VIHL QENEA FINVSFQMMV KDTFGEGETA AFHMKSGKTL SYVMKKQQNK GILMSVDGVS RLLVVSEKSF DSLSQDVPLK EQMRM VGYE LEHWQETVDV SEKLENMVPK EHTSDFQTRA PSYQIVKQGV ALMLFIGLFV SVLFFIVQGS MLYLRMFTEI EDTRVQ VLA LKRIGVTDKE IHSILGKQIG FLFFIPFIAG TIHAGFAYAA LSNMLNSNLF LEAVIVIFIY FVFQALYYIV TRHIYKR AV LQRM

UniProtKB: UNIPROTKB: A0AA96UNF6

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 69869
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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