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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | T.thermophilus 30S ribosome with KsgA, class K1k2 | ||||||||||||
![]() | B-factor sharpened map from the postprocess routine in Relion | ||||||||||||
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![]() | 30S subunit / KsgA / rRNA methyltransferase / RIBOSOME | ||||||||||||
Function / homology | ![]() 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding ...16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Raina R / Singh J | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases. Authors: Juhi Singh / Rahul Raina / Kutti R Vinothkumar / Ruchi Anand / ![]() Abstract: Methylation of specific nucleotides is integral for ribosomal biogenesis and also serves as a common mechanism to confer antibiotic resistance by pathogenic bacteria. Here, by determining the high- ...Methylation of specific nucleotides is integral for ribosomal biogenesis and also serves as a common mechanism to confer antibiotic resistance by pathogenic bacteria. Here, by determining the high-resolution structure of the 30S-KsgA complex by cryo-electron microscopy, a state was captured, where KsgA juxtaposes between helices h44 and h45 of the 30S ribosome, separating them, thereby enabling remodeling of the surrounded rRNA and allowing the cognate site to enter the methylation pocket. With the structure as a guide, several mutant versions of the ribosomes, where interacting bases in the catalytic helix h45 and surrounding helices h44, h24, and h27, were mutated and evaluated for their methylation efficiency revealing factors that direct the enzyme to its cognate site with high fidelity. The biochemical studies show that the three-dimensional environment of the ribosome enables the interaction of select loop regions in KsgA with the ribosome helices paramount to maintain selectivity. | ||||||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 117 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 56.5 KB 56.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.3 KB | Display | ![]() |
Images | ![]() | 45.1 KB | ||
Filedesc metadata | ![]() | 10.4 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 7.2 MB 8.1 MB 116.9 MB 6 MB 14.1 MB 98.1 MB 98 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7v2lMC ![]() 7v2mC ![]() 7v2nC ![]() 7v2oC ![]() 7v2pC ![]() 7v2qC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | B-factor sharpened map from the postprocess routine in Relion | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: One of the maps from multibody refinement from...
File | emd_31655_additional_1.map | ||||||||||||
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Annotation | One of the maps from multibody refinement from Relion. This map was used in model building | ||||||||||||
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Density Histograms |
-Additional map: One of the maps from multibody refinement from...
File | emd_31655_additional_2.map | ||||||||||||
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Annotation | One of the maps from multibody refinement from Relion. This map was used in model building | ||||||||||||
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Density Histograms |
-Additional map: Composite map of the multibody refinement from Phenix...
File | emd_31655_additional_3.map | ||||||||||||
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Annotation | Composite map of the multibody refinement from Phenix software. This map was used in model building | ||||||||||||
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Density Histograms |
-Additional map: One of the maps from multibody refinement from...
File | emd_31655_additional_4.map | ||||||||||||
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Annotation | One of the maps from multibody refinement from Relion. This map was used in model building | ||||||||||||
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Density Histograms |
-Additional map: This map was calculated using LocSpiral. This map...
File | emd_31655_additional_5.map | ||||||||||||
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Annotation | This map was calculated using LocSpiral. This map was used in model building. | ||||||||||||
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Density Histograms |
-Half map: One of the half maps from 3D refine,...
File | emd_31655_half_map_1.map | ||||||||||||
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Annotation | One of the half maps from 3D refine, used in the postprocess routine to obtain the primary map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: One of the half maps from 3D refine,...
File | emd_31655_half_map_2.map | ||||||||||||
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Annotation | One of the half maps from 3D refine, used in the postprocess routine to obtain the primary map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 30S ribosomal with bound KsgA, a RNA methyltransferase at position 2
+Supramolecule #1: 30S ribosomal with bound KsgA, a RNA methyltransferase at position 2
+Supramolecule #2: 30S ribosomal subunit
+Supramolecule #3: RNA methyltransferase
+Macromolecule #1: 16s ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14 type Z
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein Thx
+Macromolecule #22: Ribosomal RNA small subunit methyltransferase A
+Macromolecule #23: ZINC ION
-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 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: After application of the complex, 15 seconds wait time was given before blotting.. | ||||||||||
Details | ~2 micromolar concentration of ribosome+KsgA was used during freezing |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 43.0 e/Å2 Details: Total number of frames is 30. Each frame had 1.43 e/A2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 101449 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Phenix was used in real space for initial refinement. The final refinements was performed with REFMAC within ccpem |
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 80.1 |
Output model | ![]() PDB-7v2l: |