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- EMDB-10809: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10809 | |||||||||
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Title | Acinetobacter baumannii ribosome-amikacin complex - 50S subunit | |||||||||
![]() | Acinetobacter baumannii ribosome-amikacin complex - 50S subunit, post-processed map | |||||||||
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![]() | antibiotic / amikacin / translation / ribosome | |||||||||
Function / homology | ![]() large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Nicholson D / Edwards TA / O'Neill AJ / Ranson NA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics. Authors: David Nicholson / Thomas A Edwards / Alex J O'Neill / Neil A Ranson / ![]() Abstract: Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and ...Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and tigecycline are among the limited arsenal of drugs available for treatment of such infections. We present high-resolution structures of the 70S ribosome from A. baumannii in complex with these antibiotics, as determined by cryoelectron microscopy. Comparison with the ribosomes of other bacteria reveals several unique structural features at functionally important sites, including around the exit of the polypeptide tunnel and the periphery of the subunit interface. The structures also reveal the mode and site of interaction of these drugs with the ribosome. This work paves the way for the design of new inhibitors of translation to address infections caused by MDR A. baumannii. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 50.8 KB 50.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 32.4 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 10.3 KB | ||
Others | ![]() ![]() ![]() | 139.6 MB 185.6 MB 185.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 189.6 KB | Display | ![]() |
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Full document | ![]() | 189.1 KB | Display | |
Data in XML | ![]() | 503 B | Display | |
Data in CIF | ![]() | 374 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yhsMC ![]() 6ypuC ![]() 6ys5C ![]() 6ysiC ![]() 6yt9C ![]() 6ytfC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 177.7 Data #1: Motion-corrected micrographs of the 70S ribosome from the human pathogen Acinetobacter baumannii in complex with amikacin [micrographs - single frame] Data #2: Extracted particle images of the 70S ribosome from the human pathogen Acinetobacter baumannii in complex with amikacin [picked particles - multiframe - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Acinetobacter baumannii ribosome-amikacin complex - 50S subunit, post-processed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Acinetobacter baumannii ribosome-amikacin complex, consensus map filtered by...
File | emd_10809_additional.map | ||||||||||||
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Annotation | Acinetobacter baumannii ribosome-amikacin complex, consensus map filtered by local resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit, half...
File | emd_10809_half_map_1.map | ||||||||||||
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Annotation | Acinetobacter baumannii ribosome-amikacin complex - 50S subunit, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit, half...
File | emd_10809_half_map_2.map | ||||||||||||
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Annotation | Acinetobacter baumannii ribosome-amikacin complex - 50S subunit, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Acinetobacter baumannii ribosome-amikacin complex - 50S subunit
+Supramolecule #1: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: E-site tRNA
+Macromolecule #4: 50S ribosomal protein L2
+Macromolecule #5: 50S ribosomal protein L3
+Macromolecule #6: 50S ribosomal protein L4
+Macromolecule #7: 50S ribosomal protein L5
+Macromolecule #8: 50S ribosomal protein L6
+Macromolecule #9: 50S ribosomal protein L13
+Macromolecule #10: 50S ribosomal protein L14
+Macromolecule #11: 50S ribosomal protein L15
+Macromolecule #12: 50S ribosomal protein L16
+Macromolecule #13: 50S ribosomal protein L17
+Macromolecule #14: 50S ribosomal protein L18
+Macromolecule #15: 50S ribosomal protein L19
+Macromolecule #16: 50S ribosomal protein L20
+Macromolecule #17: 50S ribosomal protein L21
+Macromolecule #18: 50S ribosomal protein L22
+Macromolecule #19: 50S ribosomal protein L23
+Macromolecule #20: 50S ribosomal protein L24
+Macromolecule #21: 50S ribosomal protein L25
+Macromolecule #22: 50S ribosomal protein L27
+Macromolecule #23: 50S ribosomal protein L28
+Macromolecule #24: 50S ribosomal protein L29
+Macromolecule #25: 50S ribosomal protein L30
+Macromolecule #26: 50S ribosomal protein L32
+Macromolecule #27: 50S ribosomal protein L33
+Macromolecule #28: 50S ribosomal protein L34
+Macromolecule #29: 50S ribosomal protein L35
+Macromolecule #30: 50S ribosomal protein L36
+Macromolecule #31: MAGNESIUM ION
+Macromolecule #32: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient | ||||||
Output model | ![]() PDB-6yhs: |