+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16246 | |||||||||
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Title | ARE-ABCF VmlR2 bound to a 70S ribosome | |||||||||
Map data | Neobacillus subtilis VmlR2 in complex with 70S initiating ribosome from Bacillus subtilis. Unsharpened map from RELION 3D auto-refinement. | |||||||||
Sample |
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Keywords | ABC / ABCF / ABC-F / VmlR2 / antibiotic resistance / initiation / distorted P-tRNA / Shina-Dalgarno / Neobacillus vireti / Bacillus subtilis / RIBOSOME | |||||||||
Function / homology | Function and homology information positive regulation of rRNA processing / nucleoid / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding ...positive regulation of rRNA processing / nucleoid / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Neobacillus vireti (bacteria) / Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Crowe-McAuliffe C / Wilson DN | |||||||||
Funding support | Germany, Sweden, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR. Authors: Nozomu Obana / Hiraku Takada / Caillan Crowe-McAuliffe / Mizuki Iwamoto / Artyom A Egorov / Kelvin J Y Wu / Shinobu Chiba / Victoriia Murina / Helge Paternoga / Ben I C Tresco / Nobuhiko ...Authors: Nozomu Obana / Hiraku Takada / Caillan Crowe-McAuliffe / Mizuki Iwamoto / Artyom A Egorov / Kelvin J Y Wu / Shinobu Chiba / Victoriia Murina / Helge Paternoga / Ben I C Tresco / Nobuhiko Nomura / Andrew G Myers / Gemma C Atkinson / Daniel N Wilson / Vasili Hauryliuk / Abstract: Genome-encoded antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F subfamily (ARE-ABCFs) mediate intrinsic resistance in diverse Gram-positive bacteria. The diversity of ...Genome-encoded antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F subfamily (ARE-ABCFs) mediate intrinsic resistance in diverse Gram-positive bacteria. The diversity of chromosomally-encoded ARE-ABCFs is far from being fully experimentally explored. Here we characterise phylogenetically diverse genome-encoded ABCFs from Actinomycetia (Ard1 from Streptomyces capreolus, producer of the nucleoside antibiotic A201A), Bacilli (VmlR2 from soil bacterium Neobacillus vireti) and Clostridia (CplR from Clostridium perfringens, Clostridium sporogenes and Clostridioides difficile). We demonstrate that Ard1 is a narrow spectrum ARE-ABCF that specifically mediates self-resistance against nucleoside antibiotics. The single-particle cryo-EM structure of a VmlR2-ribosome complex allows us to rationalise the resistance spectrum of this ARE-ABCF that is equipped with an unusually long antibiotic resistance determinant (ARD) subdomain. We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate that C. difficile CplR (CDIF630_02847) synergises with the transposon-encoded 23S ribosomal RNA methyltransferase Erm to grant high levels of antibiotic resistance to the C. difficile 630 clinical isolate. Finally, assisted by uORF4u, our novel tool for detection of upstream open reading frames, we dissect the translational attenuation mechanism that controls the induction of cplR expression upon an antibiotic challenge. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16246.map.gz | 178.3 MB | EMDB map data format | |
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Header (meta data) | emd-16246-v30.xml emd-16246.xml | 73.8 KB 73.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16246_fsc.xml | 13.9 KB | Display | FSC data file |
Images | emd_16246.png | 125.2 KB | ||
Masks | emd_16246_msk_1.map | 226.3 MB | Mask map | |
Filedesc metadata | emd-16246.cif.gz | 14.7 KB | ||
Others | emd_16246_additional_1.map.gz emd_16246_half_map_1.map.gz emd_16246_half_map_2.map.gz | 44.1 MB 180 MB 180 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16246 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16246 | HTTPS FTP |
-Validation report
Summary document | emd_16246_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_16246_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_16246_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | emd_16246_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16246 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16246 | HTTPS FTP |
-Related structure data
Related structure data | 8buuMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16246.map.gz / Format: CCP4 / Size: 226.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Neobacillus subtilis VmlR2 in complex with 70S initiating ribosome from Bacillus subtilis. Unsharpened map from RELION 3D auto-refinement. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16246_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Neobacillus subtilis VmlR2 in complex with 70S initiating...
File | emd_16246_additional_1.map | ||||||||||||
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Annotation | Neobacillus subtilis VmlR2 in complex with 70S initiating ribosome from Bacillus subtilis. Map sharpened with B factor determined by Guinier analysis. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Neobacillus subtilis VmlR2 in complex with 70S initiating...
File | emd_16246_half_map_1.map | ||||||||||||
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Annotation | Neobacillus subtilis VmlR2 in complex with 70S initiating ribosome from Bacillus subtilis. Half map from RELION 3D auto-refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Neobacillus subtilis VmlR2 in complex with 70S initiating...
File | emd_16246_half_map_2.map | ||||||||||||
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Annotation | Neobacillus subtilis VmlR2 in complex with 70S initiating ribosome from Bacillus subtilis. Half map from RELION 3D auto-refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 70S ribosome with VmlR2 bound in the E site, a distorted tRNA in ...
+Supramolecule #1: 70S ribosome with VmlR2 bound in the E site, a distorted tRNA in ...
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #20: tRNA-fMet
+Macromolecule #26: mRNA
+Macromolecule #39: 16S rRNA
+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 #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: 30S ribosomal protein S2
+Macromolecule #27: 50S ribosomal protein L32
+Macromolecule #28: 50S ribosomal protein L33 1
+Macromolecule #29: 50S ribosomal protein L34
+Macromolecule #30: 50S ribosomal protein L35
+Macromolecule #31: 50S ribosomal protein L36
+Macromolecule #32: 30S ribosomal protein S6
+Macromolecule #33: 30S ribosomal protein S16
+Macromolecule #34: 30S ribosomal protein S18
+Macromolecule #35: 30S ribosomal protein S20
+Macromolecule #36: 30S ribosomal protein S4
+Macromolecule #37: 30S ribosomal protein S5
+Macromolecule #38: 30S ribosomal protein S8
+Macromolecule #40: 30S ribosomal protein S11
+Macromolecule #41: 30S ribosomal protein S12
+Macromolecule #42: 30S ribosomal protein S15
+Macromolecule #43: 30S ribosomal protein S17
+Macromolecule #44: 30S ribosomal protein S3
+Macromolecule #45: 30S ribosomal protein S7
+Macromolecule #46: 30S ribosomal protein S9
+Macromolecule #47: 30S ribosomal protein S10
+Macromolecule #48: 30S ribosomal protein S13
+Macromolecule #49: 30S ribosomal protein S14
+Macromolecule #50: 30S ribosomal protein S19
+Macromolecule #51: ExpZ
+Macromolecule #52: POTASSIUM ION
+Macromolecule #53: MAGNESIUM ION
+Macromolecule #54: ZINC ION
+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: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 28.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL Target criteria: Map-model cross correlation and MolProbity score |
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Output model | PDB-8buu: |