+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40051 | |||||||||
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Title | Methyltransferase RmtC bound to the 30S ribosomal subunit | |||||||||
Map data | phenix sharpened map | |||||||||
Sample |
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Keywords | ribosome / 30S / RmtC / 16S rRNA methyltransferase | |||||||||
Function / homology | Function and homology information 16S rRNA (guanine1405-N7)-methyltransferase / rRNA methyltransferase activity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation ...16S rRNA (guanine1405-N7)-methyltransferase / rRNA methyltransferase activity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Proteus mirabilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Srinivas P / Conn GL / Dunham CM | |||||||||
Funding support | United States, 1 items
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Citation | Journal: bioRxiv / Year: 2023 Title: 30S subunit recognition and G1405 modification by the aminoglycoside-resistance 16S ribosomal RNA methyltransferase RmtC. Authors: Pooja Srinivas / Meisam Nosrati / Natalia Zelinskaya / Debayan Dey / Lindsay R Comstock / Christine M Dunham / Graeme L Conn / Abstract: Acquired ribosomal RNA (rRNA) methylation has emerged as a significant mechanism of aminoglycoside resistance in pathogenic bacterial infections. Modification of a single nucleotide in the ribosome ...Acquired ribosomal RNA (rRNA) methylation has emerged as a significant mechanism of aminoglycoside resistance in pathogenic bacterial infections. Modification of a single nucleotide in the ribosome decoding center by the aminoglycoside-resistance 16S rRNA (m G1405) methyltransferases effectively blocks the action of all 4,6-deoxystreptamine ring-containing aminoglycosides, including the latest generation of drugs. To define the molecular basis of 30S subunit recognition and G1405 modification by these enzymes, we used a S-adenosyl-L-methionine (SAM) analog to trap the complex in a post-catalytic state to enable determination of an overall 3.0 Ã… cryo-electron microscopy structure of the m G1405 methyltransferase RmtC bound to the mature Escherichia coli 30S ribosomal subunit. This structure, together with functional analyses of RmtC variants, identifies the RmtC N-terminal domain as critical for recognition and docking of the enzyme on a conserved 16S rRNA tertiary surface adjacent to G1405 in 16S rRNA helix 44 (h44). To access the G1405 N7 position for modification, a collection of residues across one surface of RmtC, including a loop that undergoes a disorder to order transition upon 30S subunit binding, induces significant distortion of h44. This distortion flips G1405 into the enzyme active site where it is positioned for modification by two almost universally conserved RmtC residues. These studies expand our understanding of ribosome recognition by rRNA modification enzymes and present a more complete structural basis for future development of strategies to inhibit m G1405 modification to re-sensitize bacterial pathogens to aminoglycosides. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40051.map.gz | 163.4 MB | EMDB map data format | |
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Header (meta data) | emd-40051-v30.xml emd-40051.xml | 41.2 KB 41.2 KB | Display Display | EMDB header |
Images | emd_40051.png | 90.7 KB | ||
Filedesc metadata | emd-40051.cif.gz | 8.5 KB | ||
Others | emd_40051_additional_1.map.gz emd_40051_additional_2.map.gz emd_40051_additional_3.map.gz emd_40051_additional_4.map.gz emd_40051_additional_5.map.gz emd_40051_additional_6.map.gz emd_40051_half_map_1.map.gz emd_40051_half_map_2.map.gz | 228.4 MB 227.4 MB 223 MB 226.6 MB 226.8 MB 223.3 MB 22.2 MB 22.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40051 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40051 | HTTPS FTP |
-Validation report
Summary document | emd_40051_validation.pdf.gz | 594.9 KB | Display | EMDB validaton report |
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Full document | emd_40051_full_validation.pdf.gz | 594.4 KB | Display | |
Data in XML | emd_40051_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_40051_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40051 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40051 | HTTPS FTP |
-Related structure data
Related structure data | 8ghuMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40051.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | phenix sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.7984 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Relion post processed map
File | emd_40051_additional_1.map | ||||||||||||
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Annotation | Relion post processed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 30S body multi body
File | emd_40051_additional_2.map | ||||||||||||
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Annotation | 30S body multi body | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: RmtC multibody
File | emd_40051_additional_3.map | ||||||||||||
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Annotation | RmtC multibody | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 30S head multi body
File | emd_40051_additional_4.map | ||||||||||||
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Annotation | 30S head multi body | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: multi body map-30S
File | emd_40051_additional_5.map | ||||||||||||
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Annotation | multi body map-30S | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: multi body map-h44-rmtc
File | emd_40051_additional_6.map | ||||||||||||
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Annotation | multi body map-h44-rmtc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_40051_half_map_1.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_40051_half_map_2.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 16S rRNA methyltransferase RmtC bound to the 30S ribosomal subunit
+Supramolecule #1: 16S rRNA methyltransferase RmtC bound to the 30S ribosomal subunit
+Supramolecule #2: 16S rRNA (guanine(1405)-N(7))-methyltransferase
+Macromolecule #1: 16S rRNA (guanine(1405)-N(7))-methyltransferase
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6, non-modified isoform
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S12
+Macromolecule #10: 30S ribosomal protein S13
+Macromolecule #11: 30S ribosomal protein S15
+Macromolecule #12: 30S ribosomal protein S16
+Macromolecule #13: 30S ribosomal protein S17
+Macromolecule #14: 30S ribosomal protein S18
+Macromolecule #15: 30S ribosomal protein S20
+Macromolecule #2: 16S rRNA
+Macromolecule #16: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129736 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |