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Yorodumi- EMDB-20640: PmtCD peptide toxin ABC exporter in nucleotide free (apo) conformation -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20640 | |||||||||
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Title | PmtCD peptide toxin ABC exporter in nucleotide free (apo) conformation | |||||||||
Map data | PmtCD toxin peptide ABC exporter in nucleotide free (apo) conformation | |||||||||
Sample |
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Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.14 Å | |||||||||
Authors | Zeytuni N / Strynadka NCJ / Yu Z / Chou HT | |||||||||
Funding support | Canada, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20640.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-20640-v30.xml emd-20640.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20640_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_20640.png | 61 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20640 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20640 | HTTPS FTP |
-Validation report
Summary document | emd_20640_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_20640_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_20640_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20640 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20640 | HTTPS FTP |
-Related structure data
Related structure data | 6u2dC 6xfuC 6xjhC 6xjiC 20639 C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20640.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PmtCD toxin peptide ABC exporter in nucleotide free (apo) conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PmtCD
Entire | Name: PmtCD |
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Components |
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-Supramolecule #1: PmtCD
Supramolecule | Name: PmtCD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: PmtCD ABC exporter |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Molecular weight | Experimental: 120 KDa |
-Macromolecule #1: PmtD
Macromolecule | Name: PmtD / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: PmtC
Macromolecule | Name: PmtC / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: Solution made fresh from concentrated stocks and filtered | |||||||||
Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.45 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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