[English] 日本語
Yorodumi- EMDB-20121: Structure of trans-translation inhibitor bound to E. coli 70S rib... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20121 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of trans-translation inhibitor bound to E. coli 70S ribosome with P site tRNA | |||||||||
Map data | unfiltered main map | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / mRNA 5'-UTR binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / mRNA 5'-UTR binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosome binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Hoffer ED / Mehrani A / Keiler KC / Stagg SM / Dunham CM | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: trans-Translation inhibitors bind to a novel site on the ribosome and clear Neisseria gonorrhoeae in vivo. Authors: Zachary D Aron / Atousa Mehrani / Eric D Hoffer / Kristie L Connolly / Pooja Srinivas / Matthew C Torhan / John N Alumasa / Mynthia Cabrera / Divya Hosangadi / Jay S Barbor / Steven C ...Authors: Zachary D Aron / Atousa Mehrani / Eric D Hoffer / Kristie L Connolly / Pooja Srinivas / Matthew C Torhan / John N Alumasa / Mynthia Cabrera / Divya Hosangadi / Jay S Barbor / Steven C Cardinale / Steven M Kwasny / Lucas R Morin / Michelle M Butler / Timothy J Opperman / Terry L Bowlin / Ann Jerse / Scott M Stagg / Christine M Dunham / Kenneth C Keiler / Abstract: Bacterial ribosome rescue pathways that remove ribosomes stalled on mRNAs during translation have been proposed as novel antibiotic targets because they are essential in bacteria and are not ...Bacterial ribosome rescue pathways that remove ribosomes stalled on mRNAs during translation have been proposed as novel antibiotic targets because they are essential in bacteria and are not conserved in humans. We previously reported the discovery of a family of acylaminooxadiazoles that selectively inhibit trans-translation, the main ribosome rescue pathway in bacteria. Here, we report optimization of the pharmacokinetic and antibiotic properties of the acylaminooxadiazoles, producing MBX-4132, which clears multiple-drug resistant Neisseria gonorrhoeae infection in mice after a single oral dose. Single particle cryogenic-EM studies of non-stop ribosomes show that acylaminooxadiazoles bind to a unique site near the peptidyl-transfer center and significantly alter the conformation of ribosomal protein bL27, suggesting a novel mechanism for specific inhibition of trans-translation by these molecules. These results show that trans-translation is a viable therapeutic target and reveal a new conformation within the bacterial ribosome that may be critical for ribosome rescue pathways. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20121.map.gz | 196.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-20121-v30.xml emd-20121.xml | 83.2 KB 83.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20121_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_20121.png | 96.5 KB | ||
Masks | emd_20121_msk_1.map | 216 MB | Mask map | |
Others | emd_20121_additional_1.map.gz emd_20121_additional_2.map.gz emd_20121_half_map_1.map.gz emd_20121_half_map_2.map.gz | 30.5 MB 192.4 MB 170.9 MB 171.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20121 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20121 | HTTPS FTP |
-Related structure data
Related structure data | 6om6MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_20121.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | unfiltered main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.191 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_20121_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: sharpened main map
File | emd_20121_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened main map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: low-pass filtered main map
File | emd_20121_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | low-pass filtered main map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 1
File | emd_20121_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 2
File | emd_20121_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Structure of trans-translation inhibitor bound to E. coli 70S rib...
+Supramolecule #1: Structure of trans-translation inhibitor bound to E. coli 70S rib...
+Supramolecule #2: 50S subunit
+Supramolecule #3: 30S subunit
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 16S ribosomal RNA
+Macromolecule #3: 5S ribosomal RNA
+Macromolecule #4: mRNA
+Macromolecule #5: tRNA(gly)
+Macromolecule #6: 50S ribosomal protein L2
+Macromolecule #7: 50S ribosomal protein L3
+Macromolecule #8: 50S ribosomal protein L4
+Macromolecule #9: 50S ribosomal protein L5
+Macromolecule #10: 50S ribosomal protein L6
+Macromolecule #11: 50S ribosomal protein L9
+Macromolecule #12: 50S ribosomal protein L13
+Macromolecule #13: 50S ribosomal protein L14
+Macromolecule #14: 50S ribosomal protein L15
+Macromolecule #15: 50S ribosomal protein L16
+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 L31
+Macromolecule #29: 50S ribosomal protein L32
+Macromolecule #30: 50S ribosomal protein L33
+Macromolecule #31: 50S ribosomal protein L34
+Macromolecule #32: 50S ribosomal protein L35
+Macromolecule #33: 50S ribosomal protein L36
+Macromolecule #34: 30S ribosomal protein S2
+Macromolecule #35: 30S ribosomal protein S3
+Macromolecule #36: 30S ribosomal protein S4
+Macromolecule #37: 30S ribosomal protein S5
+Macromolecule #38: 30S ribosomal protein S6
+Macromolecule #39: 30S ribosomal protein S7
+Macromolecule #40: 30S ribosomal protein S8
+Macromolecule #41: 30S ribosomal protein S9
+Macromolecule #42: 30S ribosomal protein S10
+Macromolecule #43: 30S ribosomal protein S11
+Macromolecule #44: 30S ribosomal protein S12
+Macromolecule #45: 30S ribosomal protein S13
+Macromolecule #46: 30S ribosomal protein S14
+Macromolecule #47: 30S ribosomal protein S15
+Macromolecule #48: 30S ribosomal protein S16
+Macromolecule #49: 30S ribosomal protein S17
+Macromolecule #50: 30S ribosomal protein S18
+Macromolecule #51: 30S ribosomal protein S19
+Macromolecule #52: 30S ribosomal protein S20
+Macromolecule #53: 30S ribosomal protein S21
+Macromolecule #54: 50S ribosomal protein L27
+Macromolecule #55: 4-amino-N-[5-(4-ethynylphenyl)-1,3,4-oxadiazol-2-yl]benzamide
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - topology: HOLEY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 7.000000000000001e-05 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time: 3.5 seconds. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 6.5 µm / Digitization - Frames/image: 1-78 / Number grids imaged: 2 / Number real images: 2197 / Average exposure time: 19.302 sec. / Average electron dose: 58.0 e/Å2 Details: Two separate datesets were combined. The imaging parameter was the same for both datasets. Firth data-set had 1752 micrographs. Second data-set had 445 micrographs. |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |