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Yorodumi- PDB-7p7s: PoxtA-EQ2 antibiotic resistance ABCF bound to E. faecalis 70S rib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p7s | |||||||||
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Title | PoxtA-EQ2 antibiotic resistance ABCF bound to E. faecalis 70S ribosome, state II | |||||||||
Components |
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Keywords | RIBOSOME / Enterococcus faecalis / PoxtA / ABCF / antibiotic resistance protein | |||||||||
Function / homology | Function and homology information 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 ...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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Enterococcus faecalis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Crowe-McAuliffe, C. / Wilson, D.N. | |||||||||
Funding support | Germany, Sweden, 2items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics. Authors: Caillan Crowe-McAuliffe / Victoriia Murina / Kathryn Jane Turnbull / Susanne Huch / Marje Kasari / Hiraku Takada / Lilit Nersisyan / Arnfinn Sundsfjord / Kristin Hegstad / Gemma C Atkinson / ...Authors: Caillan Crowe-McAuliffe / Victoriia Murina / Kathryn Jane Turnbull / Susanne Huch / Marje Kasari / Hiraku Takada / Lilit Nersisyan / Arnfinn Sundsfjord / Kristin Hegstad / Gemma C Atkinson / Vicent Pelechano / Daniel N Wilson / Vasili Hauryliuk / Abstract: PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF). They confer resistance to oxazolidinone and phenicol antibiotics, such as linezolid and chloramphenicol, which stall ...PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF). They confer resistance to oxazolidinone and phenicol antibiotics, such as linezolid and chloramphenicol, which stall translating ribosomes when certain amino acids are present at a defined position in the nascent polypeptide chain. These proteins are often encoded on mobile genetic elements, facilitating their rapid spread amongst Gram-positive bacteria, and are thought to confer resistance by binding to the ribosome and dislodging the bound antibiotic. However, the mechanistic basis of this resistance remains unclear. Here we refine the PoxtA spectrum of action, demonstrate alleviation of linezolid-induced context-dependent translational stalling, and present cryo-electron microscopy structures of PoxtA in complex with the Enterococcus faecalis 70S ribosome. PoxtA perturbs the CCA-end of the P-site tRNA, causing it to shift by ∼4 Å out of the ribosome, corresponding to a register shift of approximately one amino acid for an attached nascent polypeptide chain. We postulate that the perturbation of the P-site tRNA by PoxtA thereby alters the conformation of the attached nascent chain to disrupt the drug binding site. #1: Journal: bioRxiv / Year: 2021 Title: Structural basis for PoxtA-mediated resistance to Phenicol and Oxazolidinone antibiotics Authors: Crowe-McAuliffe, C. / Murina, V. / Kasari, M. / Takada, H. / Turnbull, K.J. / Sundsfjord, A. / Hegstad, K. / Atkinson, G.C. / Wilson, D.N. / Hauryliuk, V. #2: Journal: mSphere / Year: 2018 Title: The Enterococcus Cassette Chromosome, a Genomic Variation Enabler in Enterococci. Authors: A Sivertsen / J Janice / T Pedersen / T M Wagner / J Hegstad / K Hegstad / Abstract: has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of ... has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of staphylococcus cassette chromosome elements SCC This novel element termed the enterococcus cassette chromosome (ECC) element was located in the 3' region of and encoded large serine recombinases similar to SCC Horizontal transfer of an ECC element termed ECC:: containing a knock-in chloramphenicol resistance determinant occurred in the presence of a conjugative plasmid. We determined the ECC:: insertion site in the 3' region of in the recipient by long-read sequencing. ECC:: also mobilized by homologous recombination through sequence identity between flanking insertion sequence (IS) elements in ECC:: and the conjugative plasmid. The genes were found in 69 of 516 genomes in GenBank. Full-length ECC elements were retrieved from 32 of these genomes. ECCs were flanked by and sites of approximately 50 bp. The sequences were found by PCR and sequencing of circularized ECCs in three strains. The genes in ECCs contained an amalgam of common and rare genes. Taken together, our data imply that ECC elements act as hot spots for genetic exchange and contribute to the large variation of accessory genes found in is a bacterium found in a great variety of environments, ranging from the clinic as a nosocomial pathogen to natural habitats such as mammalian intestines, water, and soil. They are known to exchange genetic material through horizontal gene transfer and recombination, leading to great variability of accessory genes and aiding environmental adaptation. Identifying mobile genetic elements causing sequence variation is important to understand how genetic content variation occurs. Here, a novel genetic island, the enterococcus cassette chromosome, is shown to contain a wealth of genes, which may aid in adapting to new environments. The transmission mechanism involves the only two conserved genes within ECC, , large serine recombinases that insert ECC into the host genome similarly to SCC elements found in staphylococci. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7p7s.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7p7s.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7p7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p7s_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7p7s_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7p7s_validation.xml.gz | 185.8 KB | Display | |
Data in CIF | 7p7s_validation.cif.gz | 312.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/7p7s ftp://data.pdbj.org/pub/pdb/validation_reports/p7/7p7s | HTTPS FTP |
-Related structure data
Related structure data | 13243MC 7p7qC 7p7rC 7p7tC 7p7uC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules 0
#1: Protein | Mass: 67890.656 Da / Num. of mol.: 1 / Mutation: E184Q, E471Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: poxtA / Production host: Enterococcus faecalis (bacteria) |
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+50S ribosomal protein ... , 28 types, 28 molecules 12345678FGHIJKMNOPQRSTUVWXYZ
-RNA chain , 5 types, 5 molecules ABDab
#10: RNA chain | Mass: 944000.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: GenBank: CP002621.1 |
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#11: RNA chain | Mass: 37433.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: GenBank: CP002621.1 |
#12: RNA chain | Mass: 25751.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) |
#33: RNA chain | Mass: 504222.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) |
#34: RNA chain | Mass: 6219.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) |
-30S ribosomal protein ... , 19 types, 19 molecules cdefghijklmnopqrstu
#35: Protein | Mass: 29500.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XQD8 |
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#36: Protein | Mass: 24415.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKR8 |
#37: Protein | Mass: 23273.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XRV7 |
#38: Protein | Mass: 17444.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKW0 |
#39: Protein | Mass: 11621.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKB6 |
#40: Protein | Mass: 17864.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKQ3 |
#41: Protein | Mass: 14936.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKS6 |
#42: Protein | Mass: 14271.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XSA2 |
#43: Protein | Mass: 11731.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKR5 |
#44: Protein | Mass: 13739.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKV1 |
#45: Protein | Mass: 15309.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKQ7 |
#46: Protein | Mass: 13595.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKT7 |
#47: Protein | Mass: 7172.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKT0 |
#48: Protein | Mass: 10668.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XRW3 |
#49: Protein | Mass: 10356.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XP69 |
#50: Protein | Mass: 10332.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKS3 |
#51: Protein | Mass: 9262.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKB3 |
#52: Protein | Mass: 10586.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKS0 |
#53: Protein | Mass: 8972.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XQJ7 |
-Non-polymers , 6 types, 349 molecules
#54: Chemical | #55: Chemical | ChemComp-MG / #56: Chemical | ChemComp-ZN / #57: Chemical | ChemComp-K / #58: Chemical | ChemComp-PUT / | #59: Chemical | ChemComp-SCM / | |
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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 |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Enterococcus faecalis (bacteria) | ||||||||||||||||||||||||||||
Buffer solution | pH: 9 | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Grid was prepared by four applications of elution fraction from affinity purification. | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 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 FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Average exposure time: 5 sec. / Electron dose: 30.255 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3639 |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 203231 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29875 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 102.35 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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