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Yorodumi- PDB-6htq: Stringent response control by a bifunctional RelA enzyme in the p... -
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-Basic information
Entry | Database: PDB / ID: 6htq | ||||||
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Title | Stringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosome | ||||||
Components |
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Keywords | RIBOSOME / Structure of bifunctional Rel on B. subtilis 70S | ||||||
Function / homology | Function and homology information GTP diphosphokinase activity / GTP diphosphokinase / guanosine tetraphosphate biosynthetic process / positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / kinase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...GTP diphosphokinase activity / GTP diphosphokinase / guanosine tetraphosphate biosynthetic process / positive regulation of rRNA processing / nucleoid / rRNA processing / 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 / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) Bacillus subtilis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Wilson, D.N. / Abdelshahid, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Cell Rep / Year: 2020 Title: Structural Basis for Regulation of the Opposing (p)ppGpp Synthetase and Hydrolase within the Stringent Response Orchestrator Rel. Authors: Patrick Pausch / Maha Abdelshahid / Wieland Steinchen / Heinrich Schäfer / Fabio Lino Gratani / Sven-Andreas Freibert / Christiane Wolz / Kürşad Turgay / Daniel N Wilson / Gert Bange / Abstract: The stringent response enables metabolic adaptation of bacteria under stress conditions and is governed by RelA/SpoT Homolog (RSH)-type enzymes. Long RSH-type enzymes encompass an N-terminal domain ...The stringent response enables metabolic adaptation of bacteria under stress conditions and is governed by RelA/SpoT Homolog (RSH)-type enzymes. Long RSH-type enzymes encompass an N-terminal domain (NTD) harboring the second messenger nucleotide (p)ppGpp hydrolase and synthetase activity and a stress-perceiving and regulatory C-terminal domain (CTD). CTD-mediated binding of Rel to stalled ribosomes boosts (p)ppGpp synthesis. However, how the opposing activities of the NTD are controlled in the absence of stress was poorly understood. Here, we demonstrate on the RSH-type protein Rel that the critical regulative elements reside within the TGS (ThrRS, GTPase, and SpoT) subdomain of the CTD, which associates to and represses the synthetase to concomitantly allow for activation of the hydrolase. Furthermore, we show that Rel forms homodimers, which appear to control the interaction with deacylated-tRNA, but not the enzymatic activity of Rel. Collectively, our study provides a detailed molecular view into the mechanism of stringent response repression in the absence of stress. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6htq.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6htq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6htq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6htq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6htq_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6htq_validation.xml.gz | 197.2 KB | Display | |
Data in CIF | 6htq_validation.cif.gz | 350.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/6htq ftp://data.pdbj.org/pub/pdb/validation_reports/ht/6htq | HTTPS FTP |
-Related structure data
Related structure data | 0270MC 6yxaC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-RNA chain , 6 types, 6 molecules ABavuw
#1: RNA chain | Mass: 948665.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 1150402534 |
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#2: RNA chain | Mass: 36157.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 1150402534 |
#30: RNA chain | Mass: 496854.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 225184640 |
#50: RNA chain | Mass: 28094.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
#52: RNA chain | Mass: 24486.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
#53: RNA chain | Mass: 24140.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
+50S ribosomal protein ... , 27 types, 27 molecules CDEFGJKLMNOPQRSTUVWXY12345Z
-30S ribosomal protein ... , 19 types, 19 molecules bcdefghijklmnopqrst
#31: Protein | Mass: 25027.107 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsB, BSU16490 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21464 |
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#32: Protein | Mass: 23032.318 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsC, BSU01220 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21465 |
#33: Protein | Mass: 22250.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsD, BSU29660 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21466 |
#34: Protein | Mass: 17362.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsE, spcA, BSU01330 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21467 |
#35: Protein | Mass: 10723.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsF, BSU40910 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21468 |
#36: Protein | Mass: 16885.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsG, BSU01110 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21469 |
#37: Protein | Mass: 14770.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsH, BSU01300 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12879 |
#38: Protein | Mass: 13748.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsI, BSU01500 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21470 |
#39: Protein | Mass: 10856.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsJ, tetA, BSU01150 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21471 |
#40: Protein | Mass: 11946.558 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsK, BSU01420 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P04969 |
#41: Protein | Mass: 14988.358 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsL, fun, strA, BSU01100 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21472 |
#42: Protein | Mass: 12374.300 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsM, BSU01410 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P20282 |
#43: Protein | Mass: 7132.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsN1, rpsN, rpsNA, rpsZ, BSU01290 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12878 |
#44: Protein | Mass: 10124.599 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsO, BSU16680 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21473 |
#45: Protein | Mass: 9893.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsP, BSU15990 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21474 |
#46: Protein | Mass: 9863.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsQ, BSU01250 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12874 |
#47: Protein | Mass: 7387.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsR, BSU40890 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21475 |
#48: Protein | Mass: 8990.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsS, BSU01200 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21476 |
#49: Protein | Mass: 9121.647 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpsT, yqeO, BSU25550 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21477 |
-Protein , 1 types, 1 molecules x
#51: Protein | Mass: 39164.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: relA, BSU27600 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: O54408, GTP diphosphokinase |
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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 |
-Sample preparation
Component | Name: Bacillus subtilis subsp. subtilis str. 168 / Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
Source (recombinant) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 650054 / Symmetry type: POINT |