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- EMDB-37563: Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subun... -
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Open data
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Basic information
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Title | Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subunit (body 1) of 70S ribosome, E- tRNA and RafH. | |||||||||
![]() | Mycobacterium smegmatis 50S ribosome (body 1) of 70S ribosome, E- tRNA and RafH. | |||||||||
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Function / homology | ![]() large ribosomal subunit / large ribosomal subunit rRNA binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kumar N / Sharma S / Kaushal PS | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH. Authors: Niraj Kumar / Shivani Sharma / Prem S Kaushal / ![]() Abstract: Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium ...Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium tuberculosis encounters hypoxia (low oxygen) as a major stress in the host macrophages, and upregulates the expression of RafH protein, which is crucial for its survival. The RafH, a dual domain HPF, an orthologue of bacterial long HPF (HPF), hibernates ribosome in 70S monosome form, whereas in other bacteria, the HPF induces 70S ribosome dimerization and hibernates its ribosome in 100S disome form. Here, we report the cryo- EM structure of M. smegmatis, a close homolog of M. tuberculosis, 70S ribosome in complex with the RafH factor at an overall 2.8 Å resolution. The N- terminus domain (NTD) of RafH binds to the decoding center, similarly to HPF NTD. In contrast, the C- terminus domain (CTD) of RafH, which is larger than the HPF CTD, binds to a distinct site at the platform binding center of the ribosomal small subunit. The two domain-connecting linker regions, which remain mostly disordered in earlier reported HPF structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 18 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 46.1 KB 46.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.4 KB | Display | ![]() |
Images | ![]() | 96.7 KB | ||
Filedesc metadata | ![]() | 10.1 KB | ||
Others | ![]() ![]() | 151.3 MB 151.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wicMC ![]() 8whxC ![]() 8whyC ![]() 8wi7C ![]() 8wi8C ![]() 8wi9C ![]() 8wibC ![]() 8widC ![]() 8wifC M: atomic model generated by this map C: citing same article ( |
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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
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Annotation | Mycobacterium smegmatis 50S ribosome (body 1) of 70S ribosome, E- tRNA and RafH. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Mycobacterium smegmatis 50S ribosome (body 1) of 70S...
File | emd_37563_half_map_1.map | ||||||||||||
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Annotation | Mycobacterium smegmatis 50S ribosome (body 1) of 70S ribosome, E- tRNA and RafH, half 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mycobacterium smegmatis 50S ribosome (body 1) of 70S...
File | emd_37563_half_map_2.map | ||||||||||||
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Annotation | Mycobacterium smegmatis 50S ribosome (body 1) of 70S ribosome, E- tRNA and RafH, half 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 70S ribosome + RafH protein
+Supramolecule #1: 70S ribosome + RafH protein
+Macromolecule #1: 50S ribosomal protein L2
+Macromolecule #2: 50S ribosomal protein L3
+Macromolecule #3: 50S ribosomal protein L4
+Macromolecule #4: 50S ribosomal protein L5
+Macromolecule #5: 50S ribosomal protein L6
+Macromolecule #6: 50S ribosomal protein L9
+Macromolecule #7: 50S ribosomal protein L13
+Macromolecule #8: 50S ribosomal protein L14
+Macromolecule #9: 50S ribosomal protein L15
+Macromolecule #10: 50S ribosomal protein L17
+Macromolecule #11: 50S ribosomal protein L18
+Macromolecule #12: 50S ribosomal protein L19
+Macromolecule #13: 50S ribosomal protein L20
+Macromolecule #14: 50S ribosomal protein L21
+Macromolecule #15: 50S ribosomal protein L22
+Macromolecule #16: 50S ribosomal protein L23
+Macromolecule #17: 50S ribosomal protein L24
+Macromolecule #18: 50S ribosomal protein L27
+Macromolecule #19: 50S ribosomal protein L28
+Macromolecule #20: 50S ribosomal protein L29
+Macromolecule #21: 50S ribosomal protein L30
+Macromolecule #22: 50S ribosomal protein L32
+Macromolecule #23: 50S ribosomal protein L33A
+Macromolecule #24: 50S ribosomal protein L34
+Macromolecule #25: 50S ribosomal protein L35
+Macromolecule #26: 50S ribosomal protein L31
+Macromolecule #27: 23S rRNA
+Macromolecule #28: 5S rRNA
+Macromolecule #29: E-tRNA
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 / Details: 20mM HEPES, 20mM MgCl2, 100mM NH4Cl, 3mM DTT |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 3 / Number real images: 110934 / Average exposure time: 2.0 sec. / Average electron dose: 1.34 e/Å2 |
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.real_space_refinement |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-8wic: |