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- PDB-8fr8: Structure of Mycobacterium smegmatis Rsh bound to a 70S translati... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fr8 | |||||||||
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Title | Structure of Mycobacterium smegmatis Rsh bound to a 70S translation initiation complex | |||||||||
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![]() | TRANSLATION / starvation sensing / RelA/SpoT homologue / Mycobacterium / 70S initiation complex | |||||||||
Function / homology | ![]() GTP diphosphokinase activity / GTP diphosphokinase / guanosine tetraphosphate biosynthetic process / large ribosomal subunit / kinase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity ...GTP diphosphokinase activity / GTP diphosphokinase / guanosine tetraphosphate biosynthetic process / large ribosomal subunit / kinase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / phosphorylation / mRNA binding / RNA binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å | |||||||||
![]() | Majumdar, S. / Sharma, M.R. / Manjari, S.R. / Banavali, N.K. / Agrawal, R.K. | |||||||||
Funding support | ![]()
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 209.8 KB | Display | |
Data in CIF | ![]() | 391.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 29397MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
+50S ribosomal protein ... , 32 types, 32 molecules cyN3KLMOPQRSTUVJDCWXYZ1246780xFH
-RNA chain , 5 types, 5 molecules EBAav
#3: RNA chain | Mass: 24780.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#5: RNA chain | Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 118168627 |
#9: RNA chain | Mass: 1011834.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 118168627 |
#37: RNA chain | Mass: 490111.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 118168627 |
#54: RNA chain | Mass: 6502.976 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
-30S ribosomal protein ... , 20 types, 20 molecules djbGefghiklmnpqrtuo9
#4: Protein | Mass: 9379.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSD5 |
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#6: Protein | Mass: 13374.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSL5 |
#38: Protein/peptide | Mass: 4033.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0A2G8BJD4 |
#39: Protein | Mass: 23617.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSD7 |
#40: Protein | Mass: 23284.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSL7 |
#41: Protein | Mass: 18481.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSG6 |
#42: Protein | Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0A2U9Q0X2 |
#43: Protein | Mass: 17529.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QS97 |
#44: Protein | Mass: 14361.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSG3 |
#45: Protein | Mass: 14093.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSP9 |
#46: Protein | Mass: 11252.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0A7I7K4Z0 |
#47: Protein | Mass: 12151.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSL6 |
#48: Protein | Mass: 13678.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QS96 |
#49: Protein | Mass: 10236.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QVQ3 |
#50: Protein | Mass: 12635.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QV37 |
#51: Protein | Mass: 10680.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSE0 |
#52: Protein | Mass: 9424.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0R102 |
#53: Protein | Mass: 25576.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QVB8 |
#57: Protein | Mass: 9449.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0R549 |
#58: Protein | Mass: 11661.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0R550 |
-Protein , 1 types, 1 molecules I
#55: Protein | Mass: 88057.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: relA Production host: ![]() ![]() References: UniProt: I7FCZ4 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Mycobacterium smegmatis 70S ribosome bound to Rsh, and initiator tRNA-fMet Type: RIBOSOME / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 66.59 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1928609 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36321 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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