[English] 日本語
Yorodumi- EMDB-12735: Cryo-EM map of a Bacillus subtilis MifM-stalled ribosome-nascent ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12735 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM map of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with GMPPNP-SRP bound | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information signal recognition particle / signal-recognition-particle GTPase / positive regulation of rRNA processing / 7S RNA binding / nucleoid / SRP-dependent cotranslational protein targeting to membrane / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing ...signal recognition particle / signal-recognition-particle GTPase / positive regulation of rRNA processing / 7S RNA binding / nucleoid / SRP-dependent cotranslational protein targeting to membrane / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / GTPase activity / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | Kratzat H / Berninghausen O / Beckmann R | |||||||||
Funding support | Germany, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp. Authors: Laura Czech / Christopher-Nils Mais / Hanna Kratzat / Pinku Sarmah / Pietro Giammarinaro / Sven-Andreas Freibert / Hanna Folke Esser / Joanna Musial / Otto Berninghausen / Wieland Steinchen ...Authors: Laura Czech / Christopher-Nils Mais / Hanna Kratzat / Pinku Sarmah / Pietro Giammarinaro / Sven-Andreas Freibert / Hanna Folke Esser / Joanna Musial / Otto Berninghausen / Wieland Steinchen / Roland Beckmann / Hans-Georg Koch / Gert Bange / Abstract: The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known ...The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known as (p)ppGpp. Here, we report that (p)ppGpp inhibits the signal recognition particle (SRP)-dependent protein targeting pathway, which is essential for membrane protein biogenesis and protein secretion. More specifically, (p)ppGpp binds to the SRP GTPases Ffh and FtsY, and inhibits the formation of the SRP receptor-targeting complex, which is central for the coordinated binding of the translating ribosome to the SecYEG translocon. Cryo-EM analysis of SRP bound to translating ribosomes suggests that (p)ppGpp may induce a distinct conformational stabilization of the NG domain of Ffh and FtsY in Bacillus subtilis but not in E. coli. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12735.map.gz | 89.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-12735-v30.xml emd-12735.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
Images | emd_12735.png | 94.8 KB | ||
Others | emd_12735_additional_1.map.gz emd_12735_additional_2.map.gz | 168.3 MB 20.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12735 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12735 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_12735.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: sharpened map
File | emd_12735_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: local resolution filtered map
File | emd_12735_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | local resolution filtered map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : SRP-bound MifM-stalled ribosome nascent chain complex
Entire | Name: SRP-bound MifM-stalled ribosome nascent chain complex |
---|---|
Components |
|
-Supramolecule #1: SRP-bound MifM-stalled ribosome nascent chain complex
Supramolecule | Name: SRP-bound MifM-stalled ribosome nascent chain complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#56 |
---|---|
Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
---|---|
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49287 |