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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20435 | |||||||||
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Title | Bacterial 45SRbgA ribosomal particle class B | |||||||||
![]() | 45SRbgA ribosome assembly intermediate | |||||||||
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![]() | Ribosome assembly / 50S subunit / RbgA / YlqF / RIBOSOME | |||||||||
Function / homology | ![]() positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding ...positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / DNA binding / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Ortega J / Seffouh A | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate. Authors: Amal Seffouh / Nikhil Jain / Dushyant Jahagirdar / Kaustuv Basu / Aida Razi / Xiaodan Ni / Alba Guarné / Robert A Britton / Joaquin Ortega / ![]() ![]() Abstract: Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most ...Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most bacteria. Homologs of this protein are also implicated in the assembly of the large subunit of the mitochondrial and eukaryotic ribosome. We present here the cryo-electron microscopy structure of RbgA bound to a Bacillus subtilis 50S subunit assembly intermediate (45SRbgA particle) that accumulates in cells upon RbgA depletion. Binding of RbgA at the P site of the immature particle stabilizes functionally important rRNA helices in the A and P-sites, prior to the completion of the maturation process of the subunit. The structure also reveals the location of the highly conserved N-terminal end of RbgA containing the catalytic residue Histidine 9. The derived model supports a mechanism of GTP hydrolysis, and it shows that upon interaction of RbgA with the 45SRbgA particle, Histidine 9 positions itself near the nucleotide potentially acting as the catalytic residue with minimal rearrangements. This structure represents the first visualization of the conformational changes induced by an assembly factor in a bacterial subunit intermediate. | |||||||||
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 | ![]() | 19.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 34.3 KB 34.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.9 KB | Display | ![]() |
Images | ![]() | 126.1 KB | ||
Filedesc metadata | ![]() | 9.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ppfMC ![]() 6ppkC ![]() 6pvkC 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
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Annotation | 45SRbgA ribosome assembly intermediate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.073 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 : 45SRbgA ribosomal assembly intermediate
+Supramolecule #1: 45SRbgA ribosomal assembly intermediate
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L13
+Macromolecule #7: 50S ribosomal protein L14
+Macromolecule #8: 50S ribosomal protein L15
+Macromolecule #9: 50S ribosomal protein L17
+Macromolecule #10: 50S ribosomal protein L18
+Macromolecule #11: 50S ribosomal protein L19
+Macromolecule #12: 50S ribosomal protein L20
+Macromolecule #13: 50S ribosomal protein L21
+Macromolecule #14: 50S ribosomal protein L22
+Macromolecule #15: 50S ribosomal protein L23
+Macromolecule #16: 50S ribosomal protein L24
+Macromolecule #17: 50S ribosomal protein L27
+Macromolecule #18: 50S ribosomal protein L30
+Macromolecule #19: 50S ribosomal protein L32
+Macromolecule #20: 50S ribosomal protein L29
+Macromolecule #21: 50S ribosomal protein L34
+Macromolecule #22: water
-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: 7.5 Details: 20mM Tris-HCl pH 7.5, 10mM MgCl2, 50mM NH4Cl, 1mM DTT |
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Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Details: Cryo-EM grids were prepared by applying a 3.6 microliters volume of the diluted samples to holey carbon grids (c-flat CF-2/2-2C-T) with a freshly applied additional layer of continuous thin ...Details: Cryo-EM grids were prepared by applying a 3.6 microliters volume of the diluted samples to holey carbon grids (c-flat CF-2/2-2C-T) with a freshly applied additional layer of continuous thin carbon (5-10nm). Grids were blotted for 3 seconds and with a blot force +1. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number real images: 8950 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / 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 |