+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0101 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | T. thermophilus hibernating 70S ribosome | |||||||||
Map data | Cryo-EM reconstruction of Thermus thermophilus 70S ribosome from hibernating 100S ribosome. | |||||||||
Sample |
| |||||||||
Keywords | Ribosome / hibernation / 100S dimer / cryo-EM | |||||||||
Function / homology | Function and homology information negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly ...negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus HB8 (bacteria) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.28 Å | |||||||||
Authors | Flygaard RK / Jenner LB | |||||||||
Funding support | Denmark, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism. Authors: Rasmus Kock Flygaard / Niels Boegholm / Marat Yusupov / Lasse B Jenner / Abstract: In response to cellular stresses bacteria conserve energy by dimerization of ribosomes into inactive hibernating 100S ribosome particles. Ribosome dimerization in Thermus thermophilus is facilitated ...In response to cellular stresses bacteria conserve energy by dimerization of ribosomes into inactive hibernating 100S ribosome particles. Ribosome dimerization in Thermus thermophilus is facilitated by hibernation-promoting factor (TtHPF). In this study we demonstrate high sensitivity of Tt100S formation to the levels of TtHPF and show that a 1:1 ratio leads to optimal dimerization. We report structures of the T. thermophilus 100S ribosome determined by cryo-electron microscopy to average resolutions of 4.13 Å and 4.57 Å. In addition, we present a 3.28 Å high-resolution cryo-EM reconstruction of a 70S ribosome from a hibernating ribosome dimer and reveal a role for the linker region connecting the TtHPF N- and C-terminal domains in translation inhibition by preventing Shine-Dalgarno duplex formation. Our work demonstrates that species-specific differences in the dimerization interface govern the overall conformation of the 100S ribosome particle and that for Thermus thermophilus no ribosome-ribosome interactions are involved in the interface. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0101.map.gz | 15 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0101-v30.xml emd-0101.xml | 75.6 KB 75.6 KB | Display Display | EMDB header |
Images | emd_0101.png | 89.9 KB | ||
Filedesc metadata | emd-0101.cif.gz | 12.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0101 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0101 | HTTPS FTP |
-Validation report
Summary document | emd_0101_validation.pdf.gz | 353.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0101_full_validation.pdf.gz | 353.1 KB | Display | |
Data in XML | emd_0101_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | emd_0101_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0101 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0101 | HTTPS FTP |
-Related structure data
Related structure data | 6gzqMC 0104C 0105C 6gzxC 6gzzC 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_0101.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM reconstruction of Thermus thermophilus 70S ribosome from hibernating 100S ribosome. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Thermus thermophilus 70S hibernating ribosome from 100S ribosome dimer
+Supramolecule #1: Thermus thermophilus 70S hibernating ribosome from 100S ribosome dimer
+Supramolecule #2: Thermus thermophilus 70S hibernating ribosome from 100S ribosome dimer
+Supramolecule #3: Ribosome hibernation promoting factor
+Macromolecule #1: 50S ribosomal protein L2
+Macromolecule #2: 50S ribosomal protein L3
+Macromolecule #3: 50S ribosomal protein L4
+Macromolecule #4: 50S ribosomal protein L5
+Macromolecule #5: 50S ribosomal protein L6
+Macromolecule #6: 50S ribosomal protein L9
+Macromolecule #7: 50S ribosomal protein L13
+Macromolecule #8: 50S ribosomal protein L14
+Macromolecule #9: 50S ribosomal protein L15
+Macromolecule #10: 50S ribosomal protein L16
+Macromolecule #11: 50S ribosomal protein L17
+Macromolecule #12: 50S ribosomal protein L18
+Macromolecule #13: 50S ribosomal protein L19
+Macromolecule #14: 50S ribosomal protein L20
+Macromolecule #15: 50S ribosomal protein L21
+Macromolecule #16: 50S ribosomal protein L22
+Macromolecule #17: 50S ribosomal protein L23
+Macromolecule #18: 50S ribosomal protein L24
+Macromolecule #19: 50S ribosomal protein L25
+Macromolecule #20: 50S ribosomal protein L27
+Macromolecule #21: 50S ribosomal protein L28
+Macromolecule #22: 50S ribosomal protein L29
+Macromolecule #23: 50S ribosomal protein L30
+Macromolecule #24: 50S ribosomal protein L31
+Macromolecule #25: 50S ribosomal protein L32
+Macromolecule #26: 50S ribosomal protein L33
+Macromolecule #27: 50S ribosomal protein L34
+Macromolecule #28: 50S ribosomal protein L35
+Macromolecule #31: 50S ribosomal protein L36
+Macromolecule #32: 30S ribosomal protein S2
+Macromolecule #33: 30S ribosomal protein S3
+Macromolecule #34: 30S ribosomal protein S4
+Macromolecule #35: 30S ribosomal protein S5
+Macromolecule #36: 30S ribosomal protein S6
+Macromolecule #37: 30S ribosomal protein S7
+Macromolecule #38: 30S ribosomal protein S8
+Macromolecule #39: 30S ribosomal protein S9
+Macromolecule #40: 30S ribosomal protein S10
+Macromolecule #41: 30S ribosomal protein S11
+Macromolecule #42: 30S ribosomal protein S12
+Macromolecule #43: 30S ribosomal protein S13
+Macromolecule #44: 30S ribosomal protein S14 type Z
+Macromolecule #45: 30S ribosomal protein S15
+Macromolecule #46: 30S ribosomal protein S16
+Macromolecule #47: 30S ribosomal protein S17
+Macromolecule #48: 30S ribosomal protein S18
+Macromolecule #49: 30S ribosomal protein S19
+Macromolecule #50: 30S ribosomal protein S20
+Macromolecule #51: 30S ribosomal protein Thx
+Macromolecule #52: Ribosome hibernation promoting factor
+Macromolecule #29: 23S ribosomal RNA
+Macromolecule #30: 5S ribosomal RNA
+Macromolecule #53: 16S ribosomal RNA
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.06 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45422 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |