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- EMDB-72173: ADP-bound structure of PmtCD in peptidisc -

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Basic information

Entry
Database: EMDB / ID: EMD-72173
TitleADP-bound structure of PmtCD in peptidisc
Map data
Sample
  • Complex: Hetero tetrameric complex of PmtC (2) and PmtD (2)
    • Protein or peptide: Phenol-soluble modulin export ABC transporter permease subunit PmtD
    • Protein or peptide: ABC transporter ATP-binding protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsABC transporter / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWorrall LJ / Li FKK / Hu J / Lazarski AC / Strynadka NCJ
Funding support Canada, 1 items
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, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72173.png

Downloads & links

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Map

FileDownload / File: emd_72173.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 170 pix.
= 229.5 Å		1.35 Å/pix.
x 170 pix.
= 229.5 Å		1.35 Å/pix.
x 170 pix.
= 229.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.111615166 - 0.1595188
Average (Standard dev.)0.00028504198 (±0.0048732655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 229.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72173_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72173_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hetero tetrameric complex of PmtC (2) and PmtD (2)

EntireName: Hetero tetrameric complex of PmtC (2) and PmtD (2)
Components
  • Complex: Hetero tetrameric complex of PmtC (2) and PmtD (2)
    • Protein or peptide: Phenol-soluble modulin export ABC transporter permease subunit PmtD
    • Protein or peptide: ABC transporter ATP-binding protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Hetero tetrameric complex of PmtC (2) and PmtD (2)

SupramoleculeName: Hetero tetrameric complex of PmtC (2) and PmtD (2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: Phenol-soluble modulin export ABC transporter permease subunit PmtD

MacromoleculeName: Phenol-soluble modulin export ABC transporter permease subunit PmtD
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 28.631359 KDa
Recombinant expressionOrganism: Staphylococcus aureus (bacteria)
SequenceString: VPRGSHRILN LVKYDLYSIF KSPLTYLAIL VVSSLIATQS ILMANSMDNP KHIIVYGSVF AAAKWLLLII GLMFVVKTIT RDFSQGTIQ LYMSKVKTRV GYIISKTISI ILISILFALI HYVILIVVQA SSNGKNLAFS KYVDNLWFFL IFLLFFGLFL F LITLASQK ...String:
VPRGSHRILN LVKYDLYSIF KSPLTYLAIL VVSSLIATQS ILMANSMDNP KHIIVYGSVF AAAKWLLLII GLMFVVKTIT RDFSQGTIQ LYMSKVKTRV GYIISKTISI ILISILFALI HYVILIVVQA SSNGKNLAFS KYVDNLWFFL IFLLFFGLFL F LITLASQK TAMIFSLGVF LVLIVPFIKP FITFIPRYGE KVLDAFDYIP FAYLTDKMIS SNFDFSNWQW VISLGSIVIF FI LNILYVA KKDI

UniProtKB: Phenol-soluble modulin export ABC transporter permease subunit PmtD

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Macromolecule #2: ABC transporter ATP-binding protein

MacromoleculeName: ABC transporter ATP-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 33.001098 KDa
Recombinant expressionOrganism: Staphylococcus aureus (bacteria)
SequenceString: MKLEHITKKY GSNVVLNDID FDFGDSRIVG LIGKNGVGKT TVMKVMNGNI IKFDGKVDID NADNIGFLIE HPKLYDNKSG LYNLKLFAQ VLGKGFDKAY TDKIIDAFGM RPYIKKKVKK YSMGMKQKLA IAVSLMNKPK FLILDEPTNG MDPDGSIDVL T TIKSLVNE ...String:
MKLEHITKKY GSNVVLNDID FDFGDSRIVG LIGKNGVGKT TVMKVMNGNI IKFDGKVDID NADNIGFLIE HPKLYDNKSG LYNLKLFAQ VLGKGFDKAY TDKIIDAFGM RPYIKKKVKK YSMGMKQKLA IAVSLMNKPK FLILDEPTNG MDPDGSIDVL T TIKSLVNE LDMRILISSH KLEDIELICD RAVFLRDGHF VQDVNMEEGV ASDTTIVTVD HKDFDRTEKY LAEHFQLQNV DK ADGHLMI NAQKNYQVIL KALSELDIYP KYIETRKSSL RDTYFNINQR GDK

UniProtKB: ABC transporter ATP-binding protein

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / 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: 8.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 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: PDB ENTRY
PDB model - PDB ID:

6xji

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 142155
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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