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- PDB-9q2q: Nucleotide-free structure of PmtCD in peptidisc -

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Basic information

Entry
Database: PDB / ID: 9q2q
TitleNucleotide-free structure of PmtCD in peptidisc
Components
  • ABC transporter ATP-binding protein
  • Phenol-soluble modulin export ABC transporter permease subunit PmtD
KeywordsMEMBRANE PROTEIN / ABC transporter
Function / homology
Function and homology information


ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC-2 family transporter protein / ABC-2 family transporter protein / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Phenol-soluble modulin export ABC transporter permease subunit PmtD / ABC transporter ATP-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWorrall, L.J. / Li, F.K.K. / Hu, J. / Lazarski, A.C. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Commun Biol / Year: 2025
Title: Cryo-EM analysis of the Staphylococcus aureus phenol-soluble modulin exporter PmtCD apo form in detergent micelles, nanodiscs and peptidiscs.
Authors: Jinhong Hu / Aleksander C Lazarski / Franco K K Li / Liam J Worrall / Dylan J Burgin / Natalie Zeytuni / Seth W Dickey / Michael Otto / Natalie C J Strynadka /
Abstract: Staphylococci secrete amphipathic peptides known as phenol soluble modulins (PSMs) that play a variety of pathogenic roles including host cell membrane destruction, biofilm development, and the ...Staphylococci secrete amphipathic peptides known as phenol soluble modulins (PSMs) that play a variety of pathogenic roles including host cell membrane destruction, biofilm development, and the triggering of inflammatory responses. PSM export is facilitated by the essential ATP-binding cassette (ABC) transporter PmtCD, which also provides producer immunity toward the membrane-damaging PSMs. Here, we report cryo-EM structures of PmtCD in a nucleotide-free state using different membrane mimetics - detergent, nanodisc and peptidisc - all featuring the transmembrane domains in an open state with a remarkably expansive intervening lumen. The consistently sized lumen suggests the possibility for two α-helical amphipathic PSMs to pack and passage within. A continuous hydrophobic surface with no apparent single high affinity site is in keeping with the ability of PmtCD to export a variety of hydrophobic PSM peptide substrates. The ATP driven collapse of the PmtD lumen is consistent with the lateral access and extrusion mechanisms of related ABC transporters that translocate membrane embedded substrates. Along with a new ADP product complex and prior ATPγS-bound form, these structures provide insights into the export of PSMs and a foundation for design of trojan horse antimicrobials that target MRSA strains from within by blocking membranolytic PSM export.
History
DepositionAug 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenol-soluble modulin export ABC transporter permease subunit PmtD
C: ABC transporter ATP-binding protein
B: Phenol-soluble modulin export ABC transporter permease subunit PmtD
D: ABC transporter ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)122,8724
Polymers122,8724
Non-polymers00
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 Phenol-soluble modulin export ABC transporter permease subunit PmtD


Mass: 28435.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: D7S40_12560 / Production host: Staphylococcus aureus (bacteria) / References: UniProt: A0A641A693
#2: Protein ABC transporter ATP-binding protein / ABC transporter / ATP-binding protein / Antibiotic ABC transporter ATP-binding protein / Antibiotic ...ABC transporter / ATP-binding protein / Antibiotic ABC transporter ATP-binding protein / Antibiotic transport system ATP-binding protein / Phenol-soluble modulin export ABC transporter ATP-binding protein PmtC


Mass: 33001.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: pmtC, ybhF_2, ybhF_3, BN1321_320024, BTN44_02050, C7P97_04805, CSC83_02360, CSC87_13000, DQV53_11320, E3A28_12735, E3K14_10305, EP54_10395, EQ90_13985, ERS072840_01916, FA040_10030, FVP29_ ...Gene: pmtC, ybhF_2, ybhF_3, BN1321_320024, BTN44_02050, C7P97_04805, CSC83_02360, CSC87_13000, DQV53_11320, E3A28_12735, E3K14_10305, EP54_10395, EQ90_13985, ERS072840_01916, FA040_10030, FVP29_15965, GO677_03780, GO746_12910, GO793_05685, GO803_12450, GO805_15850, GO894_01660, HMPREF3211_02244, NCTC10654_02103, NCTC7878_02640, NCTC9944_02076, RK64_10625, SAMEA1469856_02290, SAMEA1469884_02007, SAMEA1531680_02230, SAMEA1531701_02082, SAMEA2080329_02036, SAMEA2080330_01992, SAMEA2080334_02019, SAMEA2080433_02138, SAST44_03940, SAST45_02134
Production host: Staphylococcus aureus (bacteria) / References: UniProt: X5EJW5
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: Hetero tetrameric complex of PmtC (2) and PmtD (2) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 8.8
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: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2cryoSPARC3.2particle selection
14cryoSPARC3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108661 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0088838
ELECTRON MICROSCOPYf_angle_d1.62211932
ELECTRON MICROSCOPYf_dihedral_angle_d4.4261152
ELECTRON MICROSCOPYf_chiral_restr0.0911392
ELECTRON MICROSCOPYf_plane_restr0.0081464

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