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- PDB-6xji: PmtCD ABC exporter at C1 symmetry -

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Basic information

Entry
Database: PDB / ID: 6xji
TitlePmtCD ABC exporter at C1 symmetry
Components
  • ABC transporter ATP-binding protein
  • Phenol-soluble modulin export ABC transporter permease subunit PmtD
KeywordsMEMBRANE PROTEIN / ABC transporter / ABC exporter / Peptide transort
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsZeytuni, N. / Strynadka, N.J.C. / Hu, J. / Worrall, L.J. / Chou, H. / Yu, Z.
Funding support Canada, 1items
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,0748
Polymers126,9794
Non-polymers1,0954
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 30488.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: D7S40_12560 / Plasmid: pTX17 / 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) / Plasmid: pTX17 / Production host: Staphylococcus aureus (bacteria) / References: UniProt: X5EJW5
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: PmtCD / Type: COMPLEX / Details: PmtCD ABC exporter / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: YES
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 7.4
Details: Solution made fresh from concentrated stocks and filtered
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2150 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.16 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4CTF correction
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1132044
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113197 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0068934
ELECTRON MICROSCOPYf_angle_d0.79512080
ELECTRON MICROSCOPYf_dihedral_angle_d20.6513276
ELECTRON MICROSCOPYf_chiral_restr0.0461410
ELECTRON MICROSCOPYf_plane_restr0.0051472

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