[English] 日本語
Yorodumi- PDB-7nhl: VgaA-LC, an antibiotic resistance ABCF, in complex with 70S ribos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nhl | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | VgaA-LC, an antibiotic resistance ABCF, in complex with 70S ribosome from Staphylococcus aureus | |||||||||||||||||||||
Components |
| |||||||||||||||||||||
Keywords | RIBOSOME / Antibiotic resistance element / ABCF / antibiotic resistance / ATPase / protein synthesis | |||||||||||||||||||||
Function / homology | Function and homology information large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Staphylococcus haemolyticus (bacteria) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||||||||
Authors | Crowe-McAuliffe, C. / Murina, V. / Hauryliuk, V. / Wilson, D.N. | |||||||||||||||||||||
Funding support | Germany, Sweden, Estonia, 6items
| |||||||||||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7nhl.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7nhl.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nhl_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7nhl_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7nhl_validation.xml.gz | 220.7 KB | Display | |
Data in CIF | 7nhl_validation.cif.gz | 384.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/7nhl ftp://data.pdbj.org/pub/pdb/validation_reports/nh/7nhl | HTTPS FTP |
-Related structure data
Related structure data | 12332MC 7nhkC 7nhmC 7nhnC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10683 (Title: Affinity-purified VgaA-LC in complex with 70S ribosomes from Staphylococcus aureus Data size: 241.0 Data #1: Unaligned multi-frame micrographs of VgaA-LC bound to 70S ribosome from Staphyloccous aureus [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 1 types, 1 molecules 0
#1: Protein | Mass: 63265.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus haemolyticus (bacteria) / Gene: vga(A)LC Production host: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain (production host): SH1000 / References: UniProt: A0SNL9 |
---|
-RNA chain , 5 types, 5 molecules DAaBb
#2: RNA chain | Mass: 24506.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) |
---|---|
#5: RNA chain | Mass: 946696.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: GenBank: 87201381 |
#6: RNA chain | Mass: 501711.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: GenBank: CP000253.1 |
#7: RNA chain | Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: GenBank: CP000253.1 |
#48: RNA chain | Mass: 4128.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) |
+50S ribosomal protein ... , 28 types, 28 molecules ZPGHIJKMNOQRSTUVWXY123687945
-30S ribosomal protein ... , 19 types, 19 molecules dehklopqutnjfisgmrc
#31: Protein | Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW12 |
---|---|
#32: Protein | Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FXK6 |
#33: Protein | Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: P48940 |
#34: Protein | Mass: 11598.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: A0A0D1JTN2 |
#35: Protein | Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW31 |
#36: Protein | Mass: 7246.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW19 |
#37: Protein | Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2G2Q1 |
#38: Protein | Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FZ45 |
#39: Protein | Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FXY6 |
#41: Protein | Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW10 |
#42: Protein | Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW30 |
#43: Protein | Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW39 |
#44: Protein | Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW23 |
#45: Protein | Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW20 |
#46: Protein | Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2G111 |
#47: Protein | Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2G113 |
#49: Protein | Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: P0A0H0 |
#50: Protein | Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW15 |
#51: Protein | Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FZ25 |
-Non-polymers , 4 types, 162 molecules
#54: Chemical | ChemComp-MG / #55: Chemical | #56: Chemical | ChemComp-K / #57: Chemical | ChemComp-ZN / |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 2.2 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||
Source (recombinant) | Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: SH1000 | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
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 |
---|---|
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 |
---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 165872 |
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61910 / Num. of class averages: 1 / Symmetry type: POINT |