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Yorodumi- EMDB-12332: VgaA-LC, an antibiotic resistance ABCF, in complex with 70S ribos... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12332 | |||||||||||||||||||||
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Title | VgaA-LC, an antibiotic resistance ABCF, in complex with 70S ribosome from Staphylococcus aureus | |||||||||||||||||||||
Map data | VgaA-LC in complex with 70S ribosome from Staphylococcus aureus. Filtered by local resolution. | |||||||||||||||||||||
Sample |
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Keywords | Antibiotic resistance element / ABCF / antibiotic resistance / ATPase / protein synthesis / RIBOSOME | |||||||||||||||||||||
Function / homology | Function and homology information large ribosomal subunit / 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 ...large ribosomal subunit / 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 / 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 | Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) / Staphylococcus haemolyticus (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||||||||
Authors | Crowe-McAuliffe C / Murina V | |||||||||||||||||||||
Funding support | Germany, Sweden, Estonia, 6 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12332.map.gz | 72.7 MB | EMDB map data format | |
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Header (meta data) | emd-12332-v30.xml emd-12332.xml | 91.7 KB 91.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12332_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_12332.png | 163.2 KB | ||
Filedesc metadata | emd-12332.cif.gz | 14.9 KB | ||
Others | emd_12332_additional_1.map.gz emd_12332_additional_2.map.gz emd_12332_additional_3.map.gz emd_12332_additional_4.map.gz emd_12332_additional_5.map.gz emd_12332_half_map_1.map.gz emd_12332_half_map_2.map.gz | 22.2 MB 9.2 MB 17.7 MB 7.6 MB 73.7 MB 408.9 MB 408.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12332 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12332 | HTTPS FTP |
-Validation report
Summary document | emd_12332_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_12332_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_12332_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | emd_12332_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12332 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12332 | HTTPS FTP |
-Related structure data
Related structure data | 7nhlMC 7nhkC 7nhmC 7nhnC M: atomic model generated by this map C: citing same article (ref.) |
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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
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12332.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | VgaA-LC in complex with 70S ribosome from Staphylococcus aureus. Filtered by local resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.041 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: VgaA-LC in complex with 70S ribosome from Staphylococcus...
File | emd_12332_additional_1.map | ||||||||||||
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Annotation | VgaA-LC in complex with 70S ribosome from Staphylococcus aureus. Post-processed with automatically estimated B-factor. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Multibody refinement of ribosomal small subunit body. Post-processed...
File | emd_12332_additional_2.map | ||||||||||||
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Annotation | Multibody refinement of ribosomal small subunit body. Post-processed with automatically estimated B-factor. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Multibody refinement of ribosomal large subunit. Post-processed with...
File | emd_12332_additional_3.map | ||||||||||||
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Annotation | Multibody refinement of ribosomal large subunit. Post-processed with automatically estimated B-factor. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Multibody refinement of ribosomal small subunit head with...
File | emd_12332_additional_4.map | ||||||||||||
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Annotation | Multibody refinement of ribosomal small subunit head with VgaA-LC NBDs, L1 stalk, and P-tRNA. Post-processed with automatically estimated B-factor. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: VgaA-LC in complex with 70S ribosome from Staphylococcus...
File | emd_12332_additional_5.map | ||||||||||||
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Annotation | VgaA-LC in complex with 70S ribosome from Staphylococcus aureus. Output from RELION Refine3D job. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: VgaA-LC in complex with 70S ribosome from Staphylococcus...
File | emd_12332_half_map_1.map | ||||||||||||
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Annotation | VgaA-LC in complex with 70S ribosome from Staphylococcus aureus. Half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: VgaA-LC in complex with 70S ribosome from Staphylococcus...
File | emd_12332_half_map_2.map | ||||||||||||
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Annotation | VgaA-LC in complex with 70S ribosome from Staphylococcus aureus. Half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : VgaA-LC in complex with 70S ribosome, mRNA, and distorted P-tRNA ...
+Supramolecule #1: VgaA-LC in complex with 70S ribosome, mRNA, and distorted P-tRNA ...
+Supramolecule #2: 70S ribosome
+Supramolecule #3: VgaA-LC
+Macromolecule #1: Lincosamide-streptogramin A resistance protein
+Macromolecule #3: 50S ribosomal protein L27
+Macromolecule #4: 50S ribosomal protein L16
+Macromolecule #8: 50S ribosomal protein L2
+Macromolecule #9: 50S ribosomal protein L3
+Macromolecule #10: 50S ribosomal protein L4
+Macromolecule #11: 50S ribosomal protein L5
+Macromolecule #12: 50S ribosomal protein L6
+Macromolecule #13: 50S ribosomal protein L13
+Macromolecule #14: 50S ribosomal protein L14
+Macromolecule #15: 50S ribosomal protein L15
+Macromolecule #16: 50S ribosomal protein L17
+Macromolecule #17: 50S ribosomal protein L18
+Macromolecule #18: 50S ribosomal protein L19
+Macromolecule #19: 50S ribosomal protein L20
+Macromolecule #20: 50S ribosomal protein L21
+Macromolecule #21: 50S ribosomal protein L22
+Macromolecule #22: 50S ribosomal protein L23
+Macromolecule #23: 50S ribosomal protein L24
+Macromolecule #24: 50S ribosomal protein L25
+Macromolecule #25: 50S ribosomal protein L28
+Macromolecule #26: 50S ribosomal protein L29
+Macromolecule #27: 50S ribosomal protein L30
+Macromolecule #28: 50S ribosomal protein L33 2
+Macromolecule #29: 50S ribosomal protein L35
+Macromolecule #30: 50S ribosomal protein L34
+Macromolecule #31: 30S ribosomal protein S3
+Macromolecule #32: 30S ribosomal protein S4
+Macromolecule #33: 30S ribosomal protein S7
+Macromolecule #34: 30S ribosomal protein S10
+Macromolecule #35: 30S ribosomal protein S11
+Macromolecule #36: 30S ribosomal protein S14 type Z
+Macromolecule #37: 30S ribosomal protein S15
+Macromolecule #38: 30S ribosomal protein S16
+Macromolecule #39: 30S ribosomal protein S20
+Macromolecule #40: 50S ribosomal protein L36
+Macromolecule #41: 30S ribosomal protein S19
+Macromolecule #42: 30S ribosomal protein S13
+Macromolecule #43: 30S ribosomal protein S9
+Macromolecule #44: 30S ribosomal protein S5
+Macromolecule #45: 30S ribosomal protein S8
+Macromolecule #46: 30S ribosomal protein S18
+Macromolecule #47: 30S ribosomal protein S6
+Macromolecule #49: 30S ribosomal protein S12
+Macromolecule #50: 30S ribosomal protein S17
+Macromolecule #51: 30S ribosomal protein S2
+Macromolecule #52: 50S ribosomal protein L31 type B
+Macromolecule #53: 50S ribosomal protein L32
+Macromolecule #2: P-tRNA fMet
+Macromolecule #5: 23S rRNA
+Macromolecule #6: 16S rRNA
+Macromolecule #7: 5S rRNA
+Macromolecule #48: RNA (5'-R(P*GP*GP*AP*GP*GP*UP*AP*UP*G)-3')
+Macromolecule #54: MAGNESIUM ION
+Macromolecule #55: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #56: POTASSIUM ION
+Macromolecule #57: ZINC ION
-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 R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Average electron dose: 26.3 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 |