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Yorodumi- EMDB-33096: Mycobacterium smegmatis 50S ribosomal subunit from Stationary pha... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33096 | |||||||||||||||
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Title | Mycobacterium smegmatis 50S ribosomal subunit from Stationary phase of growth | |||||||||||||||
Map data | Mycobacterium smegmatis 50S ribosomal subunit from Stationary Phase of growth | |||||||||||||||
Sample |
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Keywords | 50S Subunit / Domain IV of 23S rRNA / Alternate conformation / Helix 68 / RIBOSOME | |||||||||||||||
Function / homology | Function and homology information large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Sengupta J / Baid P | |||||||||||||||
Funding support | India, 4 items
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Citation | Journal: Int J Biol Macromol / Year: 2023 Title: Cryo-EM captures a unique conformational rearrangement in 23S rRNA helices of the Mycobacterium 50S subunit. Authors: Priya Baid / Jayati Sengupta / Abstract: Structural investigations of the ribosomes isolated from pathogenic and non-pathogenic Mycobacterium species have identified several mycobacteria-specific structural features of ribosomal RNA and ...Structural investigations of the ribosomes isolated from pathogenic and non-pathogenic Mycobacterium species have identified several mycobacteria-specific structural features of ribosomal RNA and proteins. Here, we report structural evidence of a hitherto unknown conformational switch of mycobacterium 23S rRNA helices (H54a and H67-H71). Cryo-electron microscopy (cryo-EM) structures (~3-4 Å) of the M. smegmatis (Msm) log-phase 50S ribosomal subunit revealed conformational variability in H67-H71 region of the 23S rRNA, and manifested that, while H68 possesses the usual stretched conformation in one class of the maps, another one exhibits a bulge-out, fused density of H68-H69 at the inter-subunit surface, indicating an intrinsic dynamics of these rRNA helices. Remarkably, altered conformation of H68 forming a more prominent bulge-out structure at the inter-subunit surface of the 50S subunit due to the conformational rearrangements of 23S rRNA H67-H71 region was clearly visualized in a 3 Å cryo-EM map of the 50S subunit obtained from the stationary phase ribosome dataset. The Msm50S subunit having such bulge-out conformation at the intersubunit surface would be incompatible for associating with the 30S subunit due to its inability to form major inter-subunit bridges. Evidently, availability of active 70S ribosome pool can be modulated by stabilizing either one of the H68 conformation. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33096.map.gz | 9.8 MB | EMDB map data format | |
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Header (meta data) | emd-33096-v30.xml emd-33096.xml | 52.5 KB 52.5 KB | Display Display | EMDB header |
Images | emd_33096.png | 134.4 KB | ||
Filedesc metadata | emd-33096.cif.gz | 10.8 KB | ||
Others | emd_33096_half_map_1.map.gz emd_33096_half_map_2.map.gz | 128.9 MB 128.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33096 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33096 | HTTPS FTP |
-Validation report
Summary document | emd_33096_validation.pdf.gz | 725.7 KB | Display | EMDB validaton report |
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Full document | emd_33096_full_validation.pdf.gz | 725.3 KB | Display | |
Data in XML | emd_33096_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | emd_33096_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33096 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33096 | HTTPS FTP |
-Related structure data
Related structure data | 7xamMC 7y41C 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_33096.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Mycobacterium smegmatis 50S ribosomal subunit from Stationary Phase of growth | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Half map: Mycobacterium smegmatis 50S ribosomal subunit from Stationary Phase...
File | emd_33096_half_map_1.map | ||||||||||||
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Annotation | Mycobacterium smegmatis 50S ribosomal subunit from Stationary Phase of growth Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mycobacterium smegmatis 50S ribosomal subunit from Stationary Phase...
File | emd_33096_half_map_2.map | ||||||||||||
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Annotation | Mycobacterium smegmatis 50S ribosomal subunit from Stationary Phase of growth Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mycobacterium smegmatis 50S ribosomal subunit from Stationary Pha...
+Supramolecule #1: Mycobacterium smegmatis 50S ribosomal subunit from Stationary Pha...
+Macromolecule #1: 50S ribosomal protein bL37
+Macromolecule #4: 50S ribosomal protein L2
+Macromolecule #5: 50S ribosomal protein L3
+Macromolecule #6: 50S ribosomal protein L4
+Macromolecule #7: 50S ribosomal protein L5
+Macromolecule #8: 50S ribosomal protein L6
+Macromolecule #9: 50S ribosomal protein L9
+Macromolecule #10: 50S ribosomal protein L10
+Macromolecule #11: 50S ribosomal protein L11
+Macromolecule #12: 50S ribosomal protein L13
+Macromolecule #13: 50S ribosomal protein L14
+Macromolecule #14: 50S ribosomal protein L15
+Macromolecule #15: 50S ribosomal protein L16
+Macromolecule #16: 50S ribosomal protein L17
+Macromolecule #17: 50S ribosomal protein L18
+Macromolecule #18: 50S ribosomal protein L19
+Macromolecule #19: 50S ribosomal protein L20
+Macromolecule #20: 50S ribosomal protein L21
+Macromolecule #21: 50S ribosomal protein L22
+Macromolecule #22: 50S ribosomal protein L23
+Macromolecule #23: 50S ribosomal protein L24
+Macromolecule #24: 50S ribosomal protein L25
+Macromolecule #25: 50S ribosomal protein L27
+Macromolecule #26: 50S ribosomal protein L28
+Macromolecule #27: 50S ribosomal protein L29
+Macromolecule #28: 50S ribosomal protein L30
+Macromolecule #29: 50S ribosomal protein L32
+Macromolecule #30: 50S ribosomal protein L33 1
+Macromolecule #31: 50S ribosomal protein L34
+Macromolecule #32: 50S ribosomal protein L35
+Macromolecule #33: 50S ribosomal protein L36
+Macromolecule #34: 50S ribosomal protein L31
+Macromolecule #2: 23S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #35: MAGNESIUM ION
+Macromolecule #36: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |