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- EMDB-22194: PmtCD in peptidisc -

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ID or keywords:


Basic information

Database: EMDB / ID: EMD-22194
TitlePmtCD in peptidisc
Map data
PmtC / PmtD
Function / homology
Function and homology information

Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / transmembrane transport / ATPase activity / integral component of membrane / ATP binding / plasma membrane
ABC transporter-like / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / ABC-2 family transporter protein
Phenol-soluble modulin export ABC transporter permease subunit PmtD / ABC transporter ATP-binding protein
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsZeytuni N / Hu J / Worrall LJ / Strynadka NCJ
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)Operating grant Canada
CitationJournal: Sci Adv / Year: 2020
Title: Structural insight into the ATP-driven exporter of virulent peptide toxins.
Authors: N Zeytuni / S W Dickey / J Hu / H T Chou / L J Worrall / J A N Alexander / M L Carlson / M Nosella / F Duong / Z Yu / M Otto / N C J Strynadka /
Abstract: is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs ... is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs are amphipathic, membrane-destructive cytolytic peptides that are exported to the host-cell environment by a designated adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter, the PSM transporter (PmtABCD). Here, we demonstrate that the minimal Pmt unit necessary for PSM export is PmtCD and provide its first atomic characterization by single-particle cryo-EM and x-ray crystallography. We have captured the transporter in the ATP-bound state at near atomic resolution, revealing a type II ABC exporter fold, with an additional cytosolic domain. Comparison to a lower-resolution nucleotide-free map displaying an "open" conformation and putative hydrophobic inner chamber of a size able to accommodate the binding of two PSM peptides provides mechanistic insight and sets the foundation for therapeutic design.
DepositionJun 21, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: RCSB / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0355
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0355
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_22194.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 150 pix.
= 196.5 Å
1.31 Å/pix.
x 150 pix.
= 196.5 Å
1.31 Å/pix.
x 150 pix.
= 196.5 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Contour LevelBy AUTHOR: 0.0355 / Movie #1: 0.0355
Minimum - Maximum-0.16970164 - 0.23830341
Average (Standard dev.)0.0007075577 (±0.007834807)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 196.49998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z196.500196.500196.500
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.1700.2380.001

Supplemental data

Sample components

Entire PmtCD

EntireName: PmtCD / Details: PmtCD ABC exporter / Number of components: 3

Component #1: protein, PmtCD

ProteinName: PmtCD / Details: PmtCD ABC exporter / Recombinant expression: No
MassExperimental: 120 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

Component #2: protein, PmtC

ProteinName: PmtC / Recombinant expression: No

Component #3: protein, PmtD

ProteinName: PmtD / Recombinant expression: No

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL
Buffer solution: Solution made fresh from concentrated stocks and filtered
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.16 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 113197
3D reconstructionSoftware: RELION / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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