[English] 日本語
![](img/lk-miru.gif)
- EMDB-12244: Bacterial 30S ribosomal subunit assembly complex state F (multibo... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-12244 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Bacterial 30S ribosomal subunit assembly complex state F (multibody refinement for body domain of 30S ribosome) | |||||||||
![]() | map from multibody refinement | |||||||||
![]() |
| |||||||||
![]() | Cryo-EM / 30S biogenesis / ribosome assembly / RbfA / RsgA / YjeQ / RimP / KsgA / RsmA / Ribosome | |||||||||
Function / homology | ![]() guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity ...guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / GDP binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.98 Å | |||||||||
![]() | Schedlbauer A / Iturrioz I | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit. Authors: Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de ...Authors: Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de Astigarraga / David Gil-Carton / Paola Fucini / Sean R Connell / ![]() ![]() Abstract: While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high- ...While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30 ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16 ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 158.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 33.4 KB 33.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.6 KB | Display | ![]() |
Images | ![]() | 128.4 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 8.6 KB | ||
Others | ![]() ![]() | 158.7 MB 158.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7boiMC ![]() 7af3C ![]() 7af5C ![]() 7af8C ![]() 7afaC ![]() 7afdC ![]() 7afhC ![]() 7afiC ![]() 7afkC ![]() 7aflC ![]() 7afnC ![]() 7afoC ![]() 7afqC ![]() 7afrC ![]() 7bodC ![]() 7boeC ![]() 7bofC ![]() 7bogC ![]() 7bohC ![]() 7narC ![]() 7nasC ![]() 7natC ![]() 7nauC ![]() 7navC ![]() 7naxC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | map from multibody refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.085 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 2
File | emd_12244_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 1
File | emd_12244_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
+Entire : Bacterial 30S ribosomal subunit assembly complex state F (multibo...
+Supramolecule #1: Bacterial 30S ribosomal subunit assembly complex state F (multibo...
+Supramolecule #2: Bacterial 30S ribosomal subunit assembly
+Macromolecule #1: 16S rRNA
+Macromolecule #2: 30S ribosomal protein S4
+Macromolecule #3: 30S ribosomal protein S5
+Macromolecule #4: 30S ribosomal protein S6
+Macromolecule #5: 30S ribosomal protein S8
+Macromolecule #6: 30S ribosomal protein S11
+Macromolecule #7: 30S ribosomal protein S12
+Macromolecule #8: 30S ribosomal protein S15
+Macromolecule #9: 30S ribosomal protein S16
+Macromolecule #10: 30S ribosomal protein S17
+Macromolecule #11: 30S ribosomal protein S18
+Macromolecule #12: 30S ribosomal protein S20
+Macromolecule #13: 30S ribosomal protein S21
+Macromolecule #14: Small ribosomal subunit biogenesis GTPase RsgA
+Macromolecule #15: MAGNESIUM ION
+Macromolecule #16: ZINC ION
+Macromolecule #17: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.8 |
---|---|
Grid | Model: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 46.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |