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- EMDB-21887: Structure of the 50S subunit of the ribosome from Methicillin Res... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21887 | |||||||||
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Title | Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with the antibiotic, tedizolid | |||||||||
![]() | post-processed map | |||||||||
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Function / homology | ![]() large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Belousoff MJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM. Authors: Alexander Wright / Kieran Deane-Alder / Edward Marschall / Rebecca Bamert / Hari Venugopal / Trevor Lithgow / David W Lupton / Matthew J Belousoff / ![]() Abstract: Linezolid and tedizolid are oxazolidinones with established clinical utility for the treatment of Gram-positive pathogens. Over time it has become apparent that even modest structural changes to the ...Linezolid and tedizolid are oxazolidinones with established clinical utility for the treatment of Gram-positive pathogens. Over time it has become apparent that even modest structural changes to the core phenyl oxazolidinone leads to drastic changes in biological activity. Consequently, the structure-activity relationship around the core oxazolidinone is constantly evolving, often reflected with new structural motifs present in nascent oxazolidinones. Herein we describe the use of cryo-electron microscopy to examine the differences in binding of several functionally different oxazolidinones in the hopes of enhanced understanding of their SAR. Tedizolid, radezolid, T145, and contezolid have been examined within the peptidyl transferase center (PTC) of the 50S ribosomal subunit from methicillin resistant . The ribosome-antibiotic complexes were resolved to a resolution of around 3 Å enabling unambiguous assignment of how each antibiotic interacts with the PTC. | |||||||||
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 | ![]() | 19.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 40.5 KB 40.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 232.4 KB | ||
Others | ![]() ![]() ![]() | 141.3 MB 141.8 MB 141.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wrsMC ![]() 6wqnC ![]() 6wqqC ![]() 6wruC 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 | post-processed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_21887_additional.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_21887_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_21887_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : 50S ribosomal subunit
+Supramolecule #1: 50S ribosomal subunit
+Macromolecule #1: 50S ribosomal protein L19
+Macromolecule #2: 50S ribosomal protein L2
+Macromolecule #3: 50S ribosomal protein L20
+Macromolecule #4: 50S ribosomal protein L21
+Macromolecule #5: uL22
+Macromolecule #6: 50S ribosomal protein L23
+Macromolecule #7: 50S ribosomal protein L24
+Macromolecule #8: uL25
+Macromolecule #9: 50S ribosomal protein L28
+Macromolecule #10: 50S ribosomal protein L29
+Macromolecule #11: 50S ribosomal protein L3
+Macromolecule #12: 50S ribosomal protein L30
+Macromolecule #13: 50S ribosomal protein L32
+Macromolecule #14: 50S ribosomal protein L33
+Macromolecule #15: 50S ribosomal protein L34
+Macromolecule #16: 50S ribosomal protein L35
+Macromolecule #17: 50S ribosomal protein L36
+Macromolecule #18: 50S ribosomal protein L4
+Macromolecule #19: 50S ribosomal protein L13
+Macromolecule #20: 50S ribosomal protein L14
+Macromolecule #21: 50S ribosomal protein L15
+Macromolecule #22: 50S ribosomal protein L16
+Macromolecule #23: 50S ribosomal protein L17
+Macromolecule #24: 50S ribosomal protein L18
+Macromolecule #27: 50S ribosomal protein L27
+Macromolecule #25: 23S rRNA
+Macromolecule #26: 5S rRNA
+Macromolecule #28: Tedizolid
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |