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- EMDB-1413: Structural aspects of RbfA action during small ribosomal subunit ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1413 | |||||||||
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Title | Structural aspects of RbfA action during small ribosomal subunit assembly. | |||||||||
![]() | Cryo-EM map of Thermus thermophilus 30S subunit and RbfA complex. | |||||||||
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Function / homology | ![]() maturation of SSU-rRNA / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.5 Å | |||||||||
![]() | Datta PP / Wilson DN / Kawazoe M / Swami NK / Kaminishi T / Sharma MR / Booth TM / Takemoto C / Fucini P / Yokoyama S / Agrawal RK | |||||||||
![]() | ![]() Title: Structural aspects of RbfA action during small ribosomal subunit assembly. Authors: Partha P Datta / Daniel N Wilson / Masahito Kawazoe / Neil K Swami / Tatsuya Kaminishi / Manjuli R Sharma / Timothy M Booth / Chie Takemoto / Paola Fucini / Shigeyuki Yokoyama / Rajendra K Agrawal / ![]() Abstract: Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ...Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a crystal structure of Thermus thermophilus (Tth) RbfA and a three-dimensional cryo-electron microscopic (EM) map of the Tth 30S*RbfA complex. RbfA binds to the 30S subunit in a position overlapping the binding sites of the A and P site tRNAs, and RbfA's functionally important C terminus extends toward the 5' end of the 16S rRNA. In the presence of RbfA, a portion of the 16S rRNA encompassing helix 44, which is known to be directly involved in mRNA decoding and tRNA binding, is displaced. These results shed light on the role played by RbfA during maturation of the 30S subunit, and also indicate how RbfA provides cells with a translational advantage under conditions of cold shock. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
Images | ![]() | 68.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 294.2 KB | Display | ![]() |
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Full document | ![]() | 293.8 KB | Display | |
Data in XML | ![]() | 5.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2r1cMC ![]() 2r1gMC ![]() 2dyjC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of Thermus thermophilus 30S subunit and RbfA complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.76 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Complex of ribosomal subunit 30S and RbfA
Entire | Name: Complex of ribosomal subunit 30S and RbfA |
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Components |
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-Supramolecule #1000: Complex of ribosomal subunit 30S and RbfA
Supramolecule | Name: Complex of ribosomal subunit 30S and RbfA / type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Theoretical: 910.9 KDa |
-Supramolecule #1: 30S small ribosomal subunit
Supramolecule | Name: 30S small ribosomal subunit / type: complex / ID: 1 / Name.synonym: 30S / Details: Thermus thermophilus / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 900 KDa |
-Macromolecule #1: Ribosome binding factor A
Macromolecule | Name: Ribosome binding factor A / type: protein_or_peptide / ID: 1 / Name.synonym: RbfA / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 10.9 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 Details: 20mM Hepes-KOH (pH7.8), 10mM Mg(OAc)2, 200 mM NH4Cl, 65 mM KCL. |
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Grid | Details: Quantifoil 300 mesh Copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: Wadworth Center own cryo-plunger fabricated on-site Method: 5ul of specimen was applied to the grid, then blotted using Whatman number 1 filter paper for 2 to 4 seconds, then plunged. |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 93 K |
Alignment procedure | Legacy - Astigmatism: Objective lends astigmatism corrected at 210x magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 131 / Average electron dose: 20 e/Å2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 50760 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Oxford cryo-transfer holder / Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 61207 |
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-Atomic model buiding 1
Software | Name: O |
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Details | Protocol: Rigid Body. The domains were fitted independently using the program O |
Refinement | Protocol: RIGID BODY FIT |
Output model | ![]() PDB-2r1c: ![]() PDB-2r1g: |