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Yorodumi- EMDB-0177: Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0177 | |||||||||||||||
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Title | Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosome | |||||||||||||||
Map data | Cryo-EM map of 70S Bacillus subtilis ribosome in complex with the ABCF protein VmlR. Sharpened by B-factor. | |||||||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of rRNA processing / nucleoid / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding ...positive regulation of rRNA processing / nucleoid / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) / Escherichia coli (E. coli) / Bacillus subtilis (strain 168) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Crowe-McAuliffe C / Graf M / Huter P / Abdelshahid M / Novacek J / Wilson DN | |||||||||||||||
Funding support | Germany, Czech Republic, 4 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Structural basis for antibiotic resistance mediated by the ABCF ATPase VmlR. Authors: Caillan Crowe-McAuliffe / Michael Graf / Paul Huter / Hiraku Takada / Maha Abdelshahid / Jiří Nováček / Victoriia Murina / Gemma C Atkinson / Vasili Hauryliuk / Daniel N Wilson / Abstract: Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In , the RPP VmlR confers resistance to lincomycin (Lnc) ...Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In , the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (S) antibiotic virginiamycin M (VgM). VmlR is an ATP-binding cassette (ABC) protein of the F type, which, like other antibiotic resistance (ARE) ABCF proteins, is thought to bind to antibiotic-stalled ribosomes and promote dissociation of the drug from its binding site. To investigate the molecular mechanism by which VmlR confers antibiotic resistance, we have determined a cryo-electron microscopy (cryo-EM) structure of an ATPase-deficient VmlR-EQ mutant in complex with a ErmDL-stalled ribosomal complex (SRC). The structure reveals that VmlR binds within the E site of the ribosome, with the antibiotic resistance domain (ARD) reaching into the peptidyltransferase center (PTC) of the ribosome and a C-terminal extension (CTE) making contact with the small subunit (SSU). To access the PTC, VmlR induces a conformational change in the P-site tRNA, shifting the acceptor arm out of the PTC and relocating the CCA end of the P-site tRNA toward the A site. Together with microbiological analyses, our study indicates that VmlR allosterically dissociates the drug from its ribosomal binding site and exhibits specificity to dislodge VgM, Lnc, and the pleuromutilin tiamulin (Tia), but not chloramphenicol (Cam), linezolid (Lnz), nor the macrolide erythromycin (Ery). | |||||||||||||||
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_0177.map.gz | 24.1 MB | EMDB map data format | |
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Header (meta data) | emd-0177-v30.xml emd-0177.xml | 74 KB 74 KB | Display Display | EMDB header |
Images | emd_0177.png | 87 KB | ||
Others | emd_0177_additional.map.gz | 85.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0177 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0177 | HTTPS FTP |
-Validation report
Summary document | emd_0177_validation.pdf.gz | 260.5 KB | Display | EMDB validaton report |
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Full document | emd_0177_full_validation.pdf.gz | 259.7 KB | Display | |
Data in XML | emd_0177_validation.xml.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0177 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0177 | HTTPS FTP |
-Related structure data
Related structure data | 6ha8MC 0176C 6ha1C 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_0177.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of 70S Bacillus subtilis ribosome in complex with the ABCF protein VmlR. Sharpened by B-factor. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.061 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Cryo-EM map of 70S Bacillus subtilis ribosome in...
File | emd_0177_additional.map | ||||||||||||
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Annotation | Cryo-EM map of 70S Bacillus subtilis ribosome in complex with the ABCF protein VmlR. Filtered by local resolution. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of translating 70S ribosome with ABCF antibiotic resistan...
+Supramolecule #1: Complex of translating 70S ribosome with ABCF antibiotic resistan...
+Supramolecule #2: Ribosome
+Supramolecule #3: Nucleotide-binding protein ExpZ
+Supramolecule #4: tRNA
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #31: mRNA
+Macromolecule #33: 16S rRNA
+Macromolecule #53: P-tRNA(Leu)
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L6
+Macromolecule #8: 50S ribosomal protein L13
+Macromolecule #9: 50S ribosomal protein L14
+Macromolecule #10: 50S ribosomal protein L15
+Macromolecule #11: 50S ribosomal protein L16
+Macromolecule #12: 50S ribosomal protein L17
+Macromolecule #13: 50S ribosomal protein L18
+Macromolecule #14: 50S ribosomal protein L19
+Macromolecule #15: 50S ribosomal protein L20
+Macromolecule #16: 50S ribosomal protein L21
+Macromolecule #17: 50S ribosomal protein L22
+Macromolecule #18: 50S ribosomal protein L23
+Macromolecule #19: 50S ribosomal protein L24
+Macromolecule #20: Nucleotide-binding protein ExpZ
+Macromolecule #21: 50S ribosomal protein L27
+Macromolecule #22: 50S ribosomal protein L28
+Macromolecule #23: 50S ribosomal protein L29
+Macromolecule #24: 50S ribosomal protein L30
+Macromolecule #25: 50S ribosomal protein L32
+Macromolecule #26: 50S ribosomal protein L33 1
+Macromolecule #27: 50S ribosomal protein L34
+Macromolecule #28: 50S ribosomal protein L35
+Macromolecule #29: 50S ribosomal protein L36
+Macromolecule #30: 50S ribosomal protein L31
+Macromolecule #32: 50S ribosomal protein L1
+Macromolecule #34: 30S ribosomal protein S2
+Macromolecule #35: 30S ribosomal protein S3
+Macromolecule #36: 30S ribosomal protein S4
+Macromolecule #37: 30S ribosomal protein S5
+Macromolecule #38: 30S ribosomal protein S6
+Macromolecule #39: 30S ribosomal protein S7
+Macromolecule #40: 30S ribosomal protein S8
+Macromolecule #41: 30S ribosomal protein S9
+Macromolecule #42: 30S ribosomal protein S10
+Macromolecule #43: 30S ribosomal protein S11
+Macromolecule #44: 30S ribosomal protein S12
+Macromolecule #45: 30S ribosomal protein S13
+Macromolecule #46: 30S ribosomal protein S14
+Macromolecule #47: 30S ribosomal protein S15
+Macromolecule #48: 30S ribosomal protein S16
+Macromolecule #49: 30S ribosomal protein S17
+Macromolecule #50: 30S ribosomal protein S18
+Macromolecule #51: 30S ribosomal protein S19
+Macromolecule #52: 30S ribosomal protein S20
+Macromolecule #54: TELITHROMYCIN
+Macromolecule #55: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.425 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 | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6ha8: |