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- EMDB-22211: PmtCD ABC exporter at C1 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-22211
TitlePmtCD ABC exporter at C1 symmetry
Map data
Sample
  • Complex: PmtCD
    • Protein or peptide: Phenol-soluble modulin export ABC transporter permease subunit PmtD
    • Protein or peptide: ABC transporter ATP-binding protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsABC transporter / ABC exporter / Peptide transort / MEMBRANE PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / 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 permease / ABC transporter ATP-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsZeytuni N / Strynadka NJC / Hu J / Worrall LJ
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.
History
DepositionJun 23, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0552
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0552
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xji
  • Surface level: 0.0552
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22211.png

Downloads & links

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Map

FileDownload / File: emd_22211.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.0552 / Movie #1: 0.0552
Minimum - Maximum-0.17909151 - 0.2592474
Average (Standard dev.)0.0004033437 (±0.008725414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
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
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.1790.2590.000

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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: Phenol-soluble modulin export ABC transporter permease subunit PmtD
    • Protein or peptide: ABC transporter ATP-binding protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: PmtCD

SupramoleculeName: PmtCD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: PmtCD ABC exporter
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 120 KDa

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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: 30.488379 KDa
Recombinant expressionOrganism: Staphylococcus aureus (bacteria)
SequenceString: MHHHHHHHHH HSSGLVPRGS HRILNLVKYD LYSIFKSPLT YLAILVVSSL IATQSILMAN SMDNPKHIIV YGSVFAAAKW LLLIIGLMF VVKTITRDFS QGTIQLYMSK VKTRVGYIIS KTISIILISI LFALIHYVIL IVVQASSNGK NLAFSKYVDN L WFFLIFLL ...String:
MHHHHHHHHH HSSGLVPRGS HRILNLVKYD LYSIFKSPLT YLAILVVSSL IATQSILMAN SMDNPKHIIV YGSVFAAAKW LLLIIGLMF VVKTITRDFS QGTIQLYMSK VKTRVGYIIS KTISIILISI LFALIHYVIL IVVQASSNGK NLAFSKYVDN L WFFLIFLL FFGLFLFLIT LASQKTAMIF SLGVFLVLIV PFIKPFITFI PRYGEKVLDA FDYIPFAYLT DKMISSNFDF SN WQWVISL GSIVIFFILN ILYVAKKDI

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: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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 chloridesodium chloride

Details: Solution made fresh from concentrated stocks and filtered
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.16 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1132044
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 113197
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6xji:
PmtCD ABC exporter at C1 symmetry

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