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Yorodumi- EMDB-29397: Structure of Mycobacterium smegmatis Rsh bound to a 70S translati... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29397 | |||||||||
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Title | Structure of Mycobacterium smegmatis Rsh bound to a 70S translation initiation complex | |||||||||
Map data | M. smegmatis 70S-Rsh-fMet-tRNA complex | |||||||||
Sample |
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Keywords | starvation sensing / RelA/SpoT homologue / Mycobacterium / 70S initiation complex / TRANSLATION | |||||||||
Function / homology | Function and homology information GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / small ribosomal subunit rRNA binding / large ribosomal subunit / kinase activity / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity ...GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / small ribosomal subunit rRNA binding / large ribosomal subunit / kinase activity / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.76 Å | |||||||||
Authors | Majumdar S / Sharma MR / Manjari SR / Banavali NK / Agrawal RK | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation. Authors: Yunlong Li / Soneya Majumdar / Ryan Treen / Manjuli R Sharma / Jamie Corro / Howard B Gamper / Swati R Manjari / Jerome Prusa / Nilesh K Banavali / Christina L Stallings / Ya-Ming Hou / ...Authors: Yunlong Li / Soneya Majumdar / Ryan Treen / Manjuli R Sharma / Jamie Corro / Howard B Gamper / Swati R Manjari / Jerome Prusa / Nilesh K Banavali / Christina L Stallings / Ya-Ming Hou / Rajendra K Agrawal / Anil K Ojha / Abstract: The stringent response, which leads to persistence of nutrient-starved mycobacteria, is induced by activation of the RelA/SpoT homolog (Rsh) upon entry of a deacylated-tRNA in a translating ribosome. ...The stringent response, which leads to persistence of nutrient-starved mycobacteria, is induced by activation of the RelA/SpoT homolog (Rsh) upon entry of a deacylated-tRNA in a translating ribosome. However, the mechanism by which Rsh identifies such ribosomes in vivo remains unclear. Here, we show that conditions inducing ribosome hibernation result in loss of intracellular Rsh in a Clp protease-dependent manner. This loss is also observed in nonstarved cells using mutations in Rsh that block its interaction with the ribosome, indicating that Rsh association with the ribosome is important for Rsh stability. The cryo-EM structure of the Rsh-bound 70S ribosome in a translation initiation complex reveals unknown interactions between the ACT domain of Rsh and components of the ribosomal L7/L12 stalk base, suggesting that the aminoacylation status of A-site tRNA is surveilled during the first cycle of elongation. Altogether, we propose a surveillance model of Rsh activation that originates from its constitutive interaction with the ribosomes entering the translation cycle. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29397.map.gz | 380.8 MB | EMDB map data format | |
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Header (meta data) | emd-29397-v30.xml emd-29397.xml | 78.9 KB 78.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29397_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_29397.png | 36.7 KB | ||
Filedesc metadata | emd-29397.cif.gz | 15 KB | ||
Others | emd_29397_additional_1.map.gz emd_29397_half_map_1.map.gz emd_29397_half_map_2.map.gz | 374 MB 382.1 MB 382.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29397 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29397 | HTTPS FTP |
-Validation report
Summary document | emd_29397_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_29397_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_29397_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | emd_29397_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29397 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29397 | HTTPS FTP |
-Related structure data
Related structure data | 8fr8MC 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_29397.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | M. smegmatis 70S-Rsh-fMet-tRNA complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84744 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: M. smegmatis 70S-Rsh-fMet-tRNA complex- Composite Map
File | emd_29397_additional_1.map | ||||||||||||
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Annotation | M. smegmatis 70S-Rsh-fMet-tRNA complex- Composite Map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: M. smegmatis 70S-Rsh-fMet-tRNA complex half map 1
File | emd_29397_half_map_1.map | ||||||||||||
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Annotation | M. smegmatis 70S-Rsh-fMet-tRNA complex half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: M. smegmatis 70S-Rsh-fMet-tRNA complex half map 1
File | emd_29397_half_map_2.map | ||||||||||||
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Annotation | M. smegmatis 70S-Rsh-fMet-tRNA complex half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mycobacterium smegmatis 70S ribosome bound to Rsh, and initiator ...
+Supramolecule #1: Mycobacterium smegmatis 70S ribosome bound to Rsh, and initiator ...
+Macromolecule #1: 50S ribosomal protein L33 2
+Macromolecule #2: 50S ribosomal protein L28
+Macromolecule #4: 30S ribosomal protein S19
+Macromolecule #6: 30S ribosomal protein S13
+Macromolecule #7: 50S ribosomal protein L16
+Macromolecule #8: 50S ribosomal protein eL31
+Macromolecule #10: 50S ribosomal protein L2
+Macromolecule #11: 50S ribosomal protein L3
+Macromolecule #12: 50S ribosomal protein L4
+Macromolecule #13: 50S ribosomal protein L5
+Macromolecule #14: 50S ribosomal protein L6
+Macromolecule #15: 50S ribosomal protein L9
+Macromolecule #16: 50S ribosomal protein L10
+Macromolecule #17: 50S ribosomal protein L11
+Macromolecule #18: 50S ribosomal protein L13
+Macromolecule #19: 50S ribosomal protein L14
+Macromolecule #20: 50S ribosomal protein L15
+Macromolecule #21: 50S ribosomal protein L17
+Macromolecule #22: 50S ribosomal protein L18
+Macromolecule #23: 50S ribosomal protein L19
+Macromolecule #24: 50S ribosomal protein L20
+Macromolecule #25: 50S ribosomal protein L21
+Macromolecule #26: 50S ribosomal protein L22
+Macromolecule #27: 50S ribosomal protein L23
+Macromolecule #28: 50S ribosomal protein L24
+Macromolecule #29: 50S ribosomal protein L25
+Macromolecule #30: 50S ribosomal protein L27
+Macromolecule #31: 50S ribosomal protein L29
+Macromolecule #32: 50S ribosomal protein L30
+Macromolecule #33: 50S ribosomal protein L32
+Macromolecule #34: 50S ribosomal protein L34
+Macromolecule #35: 50S ribosomal protein L35
+Macromolecule #36: 50S ribosomal protein L36
+Macromolecule #38: 30S ribosomal protein S22
+Macromolecule #39: 30S ribosomal protein S3
+Macromolecule #40: 30S ribosomal protein S4
+Macromolecule #41: 30S ribosomal protein S5
+Macromolecule #42: 30S ribosomal protein S6
+Macromolecule #43: 30S ribosomal protein S7
+Macromolecule #44: 30S ribosomal protein S8
+Macromolecule #45: 30S ribosomal protein S9
+Macromolecule #46: 30S ribosomal protein S10
+Macromolecule #47: 30S ribosomal protein S11
+Macromolecule #48: 30S ribosomal protein S12
+Macromolecule #49: 30S ribosomal protein S15
+Macromolecule #50: 30S ribosomal protein S16
+Macromolecule #51: 30S ribosomal protein S17
+Macromolecule #52: 30S ribosomal protein S20
+Macromolecule #53: 30S ribosomal protein S2
+Macromolecule #55: GTP pyrophosphokinase RelA
+Macromolecule #56: 50S ribosomal protein L31
+Macromolecule #57: 30S ribosomal protein S18 1
+Macromolecule #58: 30S ribosomal protein S14
+Macromolecule #3: fMet tRNA (77-MER)
+Macromolecule #5: 5S rRNA (118-MER)
+Macromolecule #9: 23S rRNA (3119-MER)
+Macromolecule #37: 16S rRNA (1511-MER)
+Macromolecule #54: mRNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 66.59 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: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8fr8: |