+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22210 | |||||||||
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Title | PmtCD ABC exporter without the basket domain at C2 symmetry | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ABC transporter / ABC exporter / Peptide transort / MEMBRANE PROTEIN | |||||||||
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) / Staphylococcus aureus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Zeytuni N / Strynadka NJC / Hu J / Worrall LJ | |||||||||
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_22210.map.gz | 804.4 KB | EMDB map data format | |
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Header (meta data) | emd-22210-v30.xml emd-22210.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22210_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_22210.png | 117.5 KB | ||
Filedesc metadata | emd-22210.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22210 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22210 | HTTPS FTP |
-Validation report
Summary document | emd_22210_validation.pdf.gz | 411 KB | Display | EMDB validaton report |
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Full document | emd_22210_full_validation.pdf.gz | 410.5 KB | Display | |
Data in XML | emd_22210_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | emd_22210_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22210 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22210 | HTTPS FTP |
-Related structure data
Related structure data | 6xjhMC 6u2dC 6xfuC 6xjiC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22210.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.31 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: #1-#2 / Details: PmtCD ABC exporter |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Molecular weight | Theoretical: 120 KDa |
-Macromolecule #1: Phenol-soluble modulin export ABC transporter permease subunit PmtD
Macromolecule | Name: Phenol-soluble modulin export ABC transporter permease subunit PmtD type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Molecular weight | Theoretical: 30.488379 KDa |
Recombinant expression | Organism: Staphylococcus aureus |
Sequence | String: 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 |
-Macromolecule #2: ABC transporter ATP-binding protein
Macromolecule | Name: ABC transporter ATP-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus aureus |
Molecular weight | Theoretical: 33.001098 KDa |
Recombinant expression | Organism: Staphylococcus aureus |
Sequence | String: 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 |
-Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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 | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||
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: 1.16 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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Output model | PDB-6xjh: |