+Open data
-Basic information
Entry | Database: PDB / ID: 8buu | |||||||||
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Title | ARE-ABCF VmlR2 bound to a 70S ribosome | |||||||||
Components |
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Keywords | RIBOSOME / ABC / ABCF / ABC-F / VmlR2 / antibiotic resistance / initiation / distorted P-tRNA / Shina-Dalgarno / Neobacillus vireti / Bacillus subtilis | |||||||||
Function / homology | Function and homology information positive regulation of rRNA processing / nucleoid / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation ...positive regulation of rRNA processing / nucleoid / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Crowe-McAuliffe, C. / Wilson, D.N. | |||||||||
Funding support | Germany, Sweden, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8buu.cif.gz | 4.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8buu.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8buu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/8buu ftp://data.pdbj.org/pub/pdb/validation_reports/bu/8buu | HTTPS FTP |
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-Related structure data
Related structure data | 16246MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 5 types, 5 molecules ABVua
#1: RNA chain | Mass: 949339.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
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#2: RNA chain | Mass: 38423.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: CP053102.1 |
#20: RNA chain | Mass: 24787.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
#26: RNA chain | Mass: 4128.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
#39: RNA chain | Mass: 503353.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
+50S ribosomal protein ... , 26 types, 26 molecules CDEFGJKLMNOPQRSTUWXYZ01234
-30S ribosomal protein ... , 19 types, 19 molecules bfprtdehkloqcgijmns
#25: Protein | Mass: 28009.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: uS2 small ribosomal subunit protein Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21464 |
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#32: Protein | Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21468 |
#33: Protein | Mass: 10153.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21474 |
#34: Protein | Mass: 8990.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21475 |
#35: Protein | Mass: 9622.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21477 |
#36: Protein | Mass: 22874.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21466 |
#37: Protein | Mass: 17650.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21467 |
#38: Protein | Mass: 14901.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12879 |
#40: Protein | Mass: 13952.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P04969 |
#41: Protein | Mass: 15248.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21472 |
#42: Protein | Mass: 10597.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21473 |
#43: Protein | Mass: 10220.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12874 |
#44: Protein | Mass: 24364.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21465 |
#45: Protein | Mass: 17915.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21469 |
#46: Protein | Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21470 |
#47: Protein | Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21471 |
#48: Protein | Mass: 13818.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P20282 |
#49: Protein | Mass: 7263.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12878 |
#50: Protein | Mass: 10607.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21476 |
-Protein , 1 types, 1 molecules 9
#51: Protein | Mass: 72167.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: EQ2 variant with C-terminal his tag, Tobacco Etch Virus protease cleavage site, and FLAG tag. Source: (gene. exp.) Neobacillus vireti (bacteria) / Gene: BAVI_03309 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: W1SM44 |
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-Non-polymers , 4 types, 107 molecules
#52: Chemical | ChemComp-K / #53: Chemical | ChemComp-MG / #54: Chemical | ChemComp-ZN / #55: Chemical | |
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-Details
Has ligand of interest | N |
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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: 70S ribosome with VmlR2 bound in the E site, a distorted tRNA in the P site, and a substoichiometric distorted tRNA in the A site Type: RIBOSOME Entity ID: #25, #20, #51, #26, #1-#2, #12, #14-#16, #21-#22, #27-#31, #3-#11, #13, #17-#19, #23-#24, #32-#50 Source: RECOMBINANT |
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Molecular weight | Value: 2.5 MDa / Experimental value: NO |
Source (natural) | Organism: Neobacillus vireti (bacteria) |
Source (recombinant) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
Vitrification | 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 FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 1900 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm |
Image recording | Electron dose: 28.25 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2797082 | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140804 / Algorithm: FOURIER SPACE / Details: RELION 3D autorefine. / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Space: REAL Target criteria: Map-model cross correlation and MolProbity score | |||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.33 Å2 | |||||||||||||||||||||||||||
Refine LS restraints |
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