+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-21572 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 30S-Inactive-low-Mg2+ Class A | |||||||||
![]() | ||||||||||
![]() | 30S-Activated-high-Mg2+: nucleic-acid ![]() ![]() | |||||||||
Function / homology | ![]() mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity, mRNA regulatory element binding ...mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity, mRNA regulatory element binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Jahagirdar D / Jha V / Basu B / Gomez-Blanco J / Vargas J / Ortega J | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy. Authors: Dushyant Jahagirdar / Vikash Jha / Kaustuv Basu / Josue Gomez-Blanco / Javier Vargas / Joaquin Ortega / ![]() Abstract: It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits ...It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between an "active" and "inactive" conformation. The active conformation was described by crystallography in the early 2000s, but the structure of the inactive form at high resolution remains unsolved. Here we used cryo-electron microscopy to obtain the structure of the inactive conformation of the 30S subunit to 3.6 Å resolution and study its motions. In the inactive conformation, an alternative base-pairing of three nucleotides causes the region of helix 44, forming the decoding center to adopt an unlatched conformation and the 3' end of the 16S rRNA positions similarly to the mRNA during translation. Incubation of inactive 30S subunits at 42°C reverts these structural changes. The air-water interface to which ribosome subunits are exposed during sample preparation also peel off some ribosomal proteins. Extended exposures to low magnesium concentrations make the ribosomal particles more susceptible to the air-water interface causing the unfolding of large rRNA structural domains. Overall, this study provides new insights about the conformational space explored by the 30S ribosomal subunit when the ribosomal particles are free in solution. | |||||||||
Validation Report | ![]() ![]() ![]() ![]() | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-
Download
FSC (resolution estimation) |
|
---|---|
Header (meta data in XML format) |
|
Images |
|
![]() |
|
Archive directory |
-Related structure data
Related structure data | ![]() 6w7nCM ![]() 6w6kC ![]() 6w77C ![]() 6w7mC ![]() 6w7wC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar-shape strucutres |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.073 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire 30S-Activated-high-Mg2+
+Component #1: protein, 30S-Activated-high-Mg2+
+Component #2: nucleic-acid, 16S rRNA
+Component #3: protein, 30S ribosomal protein S3
+Component #4: protein, 30S ribosomal protein S4
+Component #5: protein, 30S ribosomal protein S5
+Component #6: protein, 30S ribosomal protein S8
+Component #7: protein, 30S ribosomal protein S9
+Component #8: protein, 30S ribosomal protein S10
+Component #9: protein, 30S ribosomal protein S12
+Component #10: protein, 30S ribosomal protein S13
+Component #11: protein, 30S ribosomal protein S14
+Component #12: protein, 30S ribosomal protein S15
+Component #13: protein, 30S ribosomal protein S16
+Component #14: protein, 30S ribosomal protein S17
+Component #15: protein, 30S ribosomal protein S19
+Component #16: protein, 30S ribosomal protein S20
-Experimental details
-
Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
---|---|
Sample solution | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
![]() | Microscope: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: FEI TITAN KRIOS AUTOGRID HOLDER |
Camera | Detector: FEI FALCON II (4k x 4k) |