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Yorodumi- PDB-7nhn: VgaL, an antibiotic resistance ABCF, in complex with 70S ribosome... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nhn | |||||||||||||||||||||
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Title | VgaL, an antibiotic resistance ABCF, in complex with 70S ribosome from Listeria monocytogenes | |||||||||||||||||||||
Components |
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Keywords | RIBOSOME / Antibiotic resistance element / ABCF / antibiotic resistance / ATPase / protein synthesis | |||||||||||||||||||||
Function / homology | Function and homology information positive regulation of translational fidelity / ATPase-coupled transmembrane transporter activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding ...positive regulation of translational fidelity / ATPase-coupled transmembrane transporter activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / large ribosomal subunit / 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 / mRNA binding / RNA binding / zinc ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Listeria monocytogenes EGD-e (bacteria) Listeria monocytogenes EGD-E (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||||||||
Authors | Crowe-McAuliffe, C. / Turnbull, K.J. / Hauryliuk, V. / Wilson, D.N. | |||||||||||||||||||||
Funding support | Germany, Sweden, Estonia, 6items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Authors: Caillan Crowe-McAuliffe / Victoriia Murina / Kathryn Jane Turnbull / Marje Kasari / Merianne Mohamad / Christine Polte / Hiraku Takada / Karolis Vaitkevicius / Jörgen Johansson / Zoya ...Authors: Caillan Crowe-McAuliffe / Victoriia Murina / Kathryn Jane Turnbull / Marje Kasari / Merianne Mohamad / Christine Polte / Hiraku Takada / Karolis Vaitkevicius / Jörgen Johansson / Zoya Ignatova / Gemma C Atkinson / Alex J O'Neill / Vasili Hauryliuk / Daniel N Wilson / Abstract: Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette ...Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaA and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms. | |||||||||||||||||||||
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 | 7nhn.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7nhn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nhn_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 7nhn_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7nhn_validation.xml.gz | 217.7 KB | Display | |
Data in CIF | 7nhn_validation.cif.gz | 378 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/7nhn ftp://data.pdbj.org/pub/pdb/validation_reports/nh/7nhn | HTTPS FTP |
-Related structure data
Related structure data | 12334MC 7nhkC 7nhlC 7nhmC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10684 (Title: Affinity-purified VgaL in complex with 70S ribosomes from Listeria monocytogenes Data size: 146.0 Data #1: Unaligned multi-frame micrographs of VgaL bound to 70S ribosome from Listeria monocytogenes [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules 0
#1: Protein | Mass: 64280.094 Da / Num. of mol.: 1 / Mutation: E104Q, E408Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria) Gene: lmo0919 / Production host: Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y8I3 |
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-RNA chain , 5 types, 5 molecules DbAaB
#2: RNA chain | Mass: 24788.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) |
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#3: RNA chain | Mass: 3783.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) |
#4: RNA chain | Mass: 949689.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) |
#5: RNA chain | Mass: 499378.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: GenBank: CP023861.1 |
#32: RNA chain | Mass: 36692.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-E (bacteria) |
+50S ribosomal protein ... , 27 types, 27 molecules GHIJKMNOPQRSTUVWXZ123567894
-30S ribosomal protein ... , 19 types, 19 molecules cdefghijklmnopqrstu
#33: Protein | Mass: 28417.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y6M6 |
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#34: Protein | Mass: 24587.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66548 |
#35: Protein | Mass: 22773.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y6T6 |
#36: Protein | Mass: 17482.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y446 |
#37: Protein | Mass: 11526.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8YAR9 |
#38: Protein | Mass: 17848.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66611 |
#39: Protein | Mass: 14667.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66623 |
#40: Protein | Mass: 14397.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y459 |
#41: Protein | Mass: 11703.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66330 |
#42: Protein | Mass: 13812.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66352 |
#43: Protein | Mass: 15216.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66372 |
#44: Protein | Mass: 13738.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66383 |
#45: Protein | Mass: 7164.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66401 |
#46: Protein | Mass: 10656.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q92C24 |
#47: Protein | Mass: 10386.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y699 |
#48: Protein | Mass: 10057.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q927L6 |
#49: Protein | Mass: 9119.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66461 |
#50: Protein | Mass: 10498.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66484 |
#51: Protein | Mass: 9189.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66503 |
-Non-polymers , 5 types, 171 molecules
#53: Chemical | #54: Chemical | ChemComp-MG / #55: Chemical | #56: Chemical | ChemComp-K / #57: 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: VgaL in complex with 70S ribosome, mRNA, and distorted P-tRNA from Listeria monocytogenes Type: RIBOSOME / Entity ID: #1-#52 / Source: RECOMBINANT |
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Molecular weight | Value: 2.2 MDa / Experimental value: NO |
Source (natural) | Organism: Listeria monocytogenes EGD-e (bacteria) |
Source (recombinant) | Organism: Listeria monocytogenes EGD-e (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: -1900 nm / Nominal defocus min: -700 nm / Cs: 2.7 mm |
Image recording | Electron dose: 26.3 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
-Processing
EM software | Name: Gctf / Category: CTF correction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 83340 |
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45548 / Symmetry type: POINT |