+Open data
-Basic information
Entry | Database: PDB / ID: 6xji | ||||||
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Title | PmtCD ABC exporter at C1 symmetry | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ABC transporter / ABC exporter / Peptide transort | ||||||
Function / homology | Function and homology information ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Zeytuni, N. / Strynadka, N.J.C. / Hu, J. / Worrall, L.J. / Chou, H. / Yu, Z. | ||||||
Funding support | Canada, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6xji.cif.gz | 209.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xji.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 6xji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xji_validation.pdf.gz | 945.7 KB | Display | wwPDB validaton report |
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Full document | 6xji_full_validation.pdf.gz | 952.7 KB | Display | |
Data in XML | 6xji_validation.xml.gz | 36 KB | Display | |
Data in CIF | 6xji_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/6xji ftp://data.pdbj.org/pub/pdb/validation_reports/xj/6xji | HTTPS FTP |
-Related structure data
Related structure data | 22211MC 6u2dC 6xfuC 6xjhC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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, UniProt: Q2FWX0*PLUS #2: Protein | 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 | #4: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PmtCD / Type: COMPLEX / Details: PmtCD ABC exporter / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.12 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: Staphylococcus aureus (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Staphylococcus aureus (bacteria) | |||||||||||||||
Buffer solution | pH: 7.4 Details: Solution made fresh from concentrated stocks and filtered | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.16 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1132044 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113197 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Refine LS restraints |
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