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Yorodumi- EMDB-10915: Acinetobacter baumannii ribosome-tigecycline complex - 30S subuni... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10915 | |||||||||
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Title | Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head | |||||||||
Map data | Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head, post-processed map | |||||||||
Sample |
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Keywords | antibiotic / tigecycline / translation / ribosome | |||||||||
Function / homology | Function and homology information ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding ...ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria) / Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Nicholson D / Edwards TA / O'Neill AJ / Ranson NA | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Structure / Year: 2020 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10915.map.gz | 12.4 MB | EMDB map data format | |
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Header (meta data) | emd-10915-v30.xml emd-10915.xml | 30.9 KB 30.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10915_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_10915.png | 11.2 KB | ||
Masks | emd_10915_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-10915.cif.gz | 7.9 KB | ||
Others | emd_10915_additional.map.gz emd_10915_half_map_1.map.gz emd_10915_half_map_2.map.gz | 141.3 MB 132.3 MB 132.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10915 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10915 | HTTPS FTP |
-Validation report
Summary document | emd_10915_validation.pdf.gz | 355.8 KB | Display | EMDB validaton report |
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Full document | emd_10915_full_validation.pdf.gz | 354.9 KB | Display | |
Data in XML | emd_10915_validation.xml.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10915 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10915 | HTTPS FTP |
-Related structure data
Related structure data | 6ytfMC 6yhsC 6ypuC 6ys5C 6ysiC 6yt9C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10407 (Title: Motion-corrected micrographs and extracted particle images of the 70S ribosome from the human pathogen Acinetobacter baumannii in complex with tigecycline Data size: 538.5 Data #1: Motion-corrected micrographs of the 70S ribosome from the human pathogen Acinetobacter baumannii in complex with tigecycline [micrographs - single frame] Data #2: Extracted particle images of the 70S ribosome from the human pathogen Acinetobacter baumannii in complex with tigecycline [picked particles - multiframe - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10915.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head, post-processed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10915_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Acinetobacter baumannii ribosome-tigecycline complex, consensus map filtered by...
File | emd_10915_additional.map | ||||||||||||
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Annotation | Acinetobacter baumannii ribosome-tigecycline complex, consensus map filtered by local resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head,...
File | emd_10915_half_map_1.map | ||||||||||||
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Annotation | Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head,...
File | emd_10915_half_map_2.map | ||||||||||||
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Annotation | Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Acinetobacter baumannii ribosome-tigecycline complex - 30S subuni...
+Supramolecule #1: Acinetobacter baumannii ribosome-tigecycline complex - 30S subuni...
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #2: E-site tRNA
+Macromolecule #3: mRNA
+Macromolecule #4: 30S ribosomal protein S3
+Macromolecule #5: 30S ribosomal protein S7
+Macromolecule #6: 30S ribosomal protein S9
+Macromolecule #7: 30S ribosomal protein S10
+Macromolecule #8: 30S ribosomal protein S13
+Macromolecule #9: 30S ribosomal protein S14
+Macromolecule #10: 30S ribosomal protein S19
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: TIGECYCLINE
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.1 sec. / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Details | The quality of the map is relatively poor so the related PDB entry 6YS5 (A. baumannii ribosome-amikacin complex - 30S subunit head) was rigid body fitted into the map using Chimera X-0.9, tigecycline was placed into the density at the primary site, and one round of global real space refinement and local refinement were carried out using PHENIX and Coot respectively, using ligand restraints in both cases. | ||||||
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient | ||||||
Output model | PDB-6ytf: |