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- EMDB-3661: RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly inte... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3661 | |||||||||
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Title | RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly intermediate) | |||||||||
![]() | Postprocessed merged map. rlnFinalResolution 5.391515_rlnBfactorUsedForSharpening -100.000000 | |||||||||
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![]() | ribosome | |||||||||
Function / homology | ![]() guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / 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 ...guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / 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 / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / GDP binding / ribosome biogenesis / 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 / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.16 Å | |||||||||
![]() | Lopez-Alonso JP / Kaminishi T | |||||||||
![]() | ![]() Title: RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket. Authors: Jorge Pedro López-Alonso / Tatsuya Kaminishi / Takeshi Kikuchi / Yuya Hirata / Idoia Iturrioz / Neha Dhimole / Andreas Schedlbauer / Yoichi Hase / Simon Goto / Daisuke Kurita / Akira Muto / ...Authors: Jorge Pedro López-Alonso / Tatsuya Kaminishi / Takeshi Kikuchi / Yuya Hirata / Idoia Iturrioz / Neha Dhimole / Andreas Schedlbauer / Yoichi Hase / Simon Goto / Daisuke Kurita / Akira Muto / Shu Zhou / Chieko Naoe / Deryck J Mills / David Gil-Carton / Chie Takemoto / Hyouta Himeno / Paola Fucini / Sean R Connell / ![]() ![]() ![]() Abstract: During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, ...During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, namely, kinetically trapped particles. Among the assembly factors, the circularly permuted GTPase, RsgA, plays a crucial role in the maturation of the 30S decoding center. Here, directed hydroxyl radical probing and single particle cryo-EM are employed to elucidate RsgA΄s mechanism of action. Our results show that RsgA destabilizes the 30S structure, including late binding r-proteins, providing a structural basis for avoiding kinetically trapped assembly intermediates. Moreover, RsgA exploits its distinct GTPase pocket and specific interactions with the 30S to coordinate GTPase activation with the maturation state of the 30S subunit. This coordination validates the architecture of the decoding center and facilitates the timely release of RsgA to control the progression of 30S biogenesis. | |||||||||
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 | ![]() | 5.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 37.7 KB 37.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 141.7 KB | ||
Filedesc metadata | ![]() | 9.4 KB | ||
Others | ![]() ![]() | 49.5 MB 49.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5no2MC ![]() 3662C ![]() 3663C ![]() 5no3C ![]() 5no4C 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 | Postprocessed merged map. rlnFinalResolution 5.391515_rlnBfactorUsedForSharpening -100.000000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half volume 1- note corrected pixel size is...
File | emd_3661_half_map_1.map | ||||||||||||
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Annotation | half volume 1- note corrected pixel size is 1.39 -use 1.39 for post processing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_3661_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 30S ribosomal subunit bound by RsgA
+Supramolecule #1: 30S ribosomal subunit bound by RsgA
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S4
+Macromolecule #3: 30S ribosomal protein S5
+Macromolecule #4: 30S ribosomal protein S6
+Macromolecule #5: 30S ribosomal protein S7
+Macromolecule #6: 30S ribosomal protein S8
+Macromolecule #7: 30S ribosomal protein S9
+Macromolecule #8: 30S ribosomal protein S10
+Macromolecule #9: 30S ribosomal protein S11
+Macromolecule #10: 30S ribosomal protein S12
+Macromolecule #11: 30S ribosomal protein S13
+Macromolecule #12: 30S ribosomal protein S14
+Macromolecule #13: 30S ribosomal protein S15
+Macromolecule #14: 30S ribosomal protein S16
+Macromolecule #15: 30S ribosomal protein S17
+Macromolecule #16: 30S ribosomal protein S18
+Macromolecule #17: 30S ribosomal protein S19
+Macromolecule #18: 30S ribosomal protein S20
+Macromolecule #19: Small ribosomal subunit biogenesis GTPase RsgA
+Macromolecule #20: MAGNESIUM ION
+Macromolecule #21: ZINC ION
+Macromolecule #22: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
-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 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK II |
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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 / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number real images: 3408 / Average exposure time: 1.5 sec. / Average electron dose: 2.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 101000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: BACKBONE TRACE |
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Output model | ![]() PDB-5no2: |