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- EMDB-20640: PmtCD peptide toxin ABC exporter in nucleotide free (apo) conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-20640
TitlePmtCD peptide toxin ABC exporter in nucleotide free (apo) conformation
Map dataPmtCD toxin peptide ABC exporter in nucleotide free (apo) conformation
Sample
  • Complex: PmtCD
    • Protein or peptide: PmtD
    • Protein or peptide: PmtC
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.14 Å
AuthorsZeytuni N / Strynadka NCJ / Yu Z / Chou HT
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health ResearchOperating 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.
History
DepositionAug 26, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseOct 14, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.391
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.391
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20640.png

Downloads & links

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Map

FileDownload / File: emd_20640.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPmtCD toxin peptide ABC exporter in nucleotide free (apo) conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 256 pix.
= 345.6 Å		1.35 Å/pix.
x 256 pix.
= 345.6 Å		1.35 Å/pix.
x 256 pix.
= 345.6 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: 0.391 / Movie #1: 0.391
Minimum - Maximum-0.5588852 - 1.2679989
Average (Standard dev.)0.0062988037 (±0.057388388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ161186271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.5591.2680.006

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Supplemental data

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Sample components

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Entire : PmtCD

EntireName: PmtCD
Components
  • Complex: PmtCD
    • Protein or peptide: PmtD
    • Protein or peptide: PmtC

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Supramolecule #1: PmtCD

SupramoleculeName: PmtCD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: PmtCD ABC exporter
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightExperimental: 120 KDa

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Macromolecule #1: PmtD

MacromoleculeName: PmtD / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Staphylococcus aureus (bacteria)
SequenceString: MRILNLVKYD FYSIFKSPLT YLAILVVSSL IATQSILMAN SMDNPKHIIV YGSVFAAAKW LLLIIGLMF VVKTITRDFS QGTIQLYMSK VKTRVGYIIS KTISIILISI LFALIHYVIL I VVQASSNG KNLAFSKYVD NLWFFLIFLL FFGLFLFLIT LASQKTAMIF ...String:
MRILNLVKYD FYSIFKSPLT YLAILVVSSL IATQSILMAN SMDNPKHIIV YGSVFAAAKW LLLIIGLMF VVKTITRDFS QGTIQLYMSK VKTRVGYIIS KTISIILISI LFALIHYVIL I VVQASSNG KNLAFSKYVD NLWFFLIFLL FFGLFLFLIT LASQKTAMIF SLGVFLVLIV PF IKPFITF IPRYGEKVLD AFDYIPFAYL TDKMISSNFD FSNWQWVISL GSIVIFFILN ILY VAKKDI

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Macromolecule #2: PmtC

MacromoleculeName: PmtC / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Staphylococcus aureus (bacteria)
SequenceString: MKLEHITKKY GSNVVLNDID FDFGDSRIVG LIGKNGVGKT TVMKVMNGNI IKFDGKVDID NADNIGFLI EHPKLYDNKS GLYNLKLFAQ VLGKGFDKAY TDKIIDAFGM RPYIKKKVKK Y SMGMKQKL AIAVSLMNKP KFLILDEPTN GMDPDGSIDV LTTIKSLVNE ...String:
MKLEHITKKY GSNVVLNDID FDFGDSRIVG LIGKNGVGKT TVMKVMNGNI IKFDGKVDID NADNIGFLI EHPKLYDNKS GLYNLKLFAQ VLGKGFDKAY TDKIIDAFGM RPYIKKKVKK Y SMGMKQKL AIAVSLMNKP KFLILDEPTN GMDPDGSIDV LTTIKSLVNE LDMRILISSH KL EDIELIC DRAVFLRDGH FVQDVNMEEG VASDTTIVTV DHKDFDRTEK YLAEHFQLQN VDK ADGHLM INAQKNYQVI LKALSELDIY PKYIETRKSS LRDTYFNINQ RGDK

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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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClsodium chloride

Details: Solution made fresh from concentrated stocks and filtered
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.45 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 440420
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 1) / Number images used: 76140
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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