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- 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 | ||||||
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![]() | RIBOSOME / Structure of bifunctional Rel on B. subtilis 70S | ||||||
Function / homology | ![]() GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / positive regulation of rRNA processing / nucleoid / response to starvation / rRNA processing / large ribosomal subunit / kinase activity ...GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / positive regulation of rRNA processing / nucleoid / response to starvation / 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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / phosphorylation / response to antibiotic / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
![]() | Wilson, D.N. / Abdelshahid, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3.2 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 197.2 KB | Display | |
Data in CIF | ![]() | 350.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0270MC ![]() 6yxaC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() Production host: ![]() ![]() 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.) ![]() ![]() Production host: ![]() ![]() 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.) ![]() ![]() Production host: ![]() ![]() 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.) ![]() ![]() Production host: ![]() ![]() |
#52: RNA chain | Mass: 24486.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
#53: RNA chain | Mass: 24140.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
+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.) ![]() ![]() Strain: 168 / Gene: rpsB, BSU16490 Production host: ![]() ![]() 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.) ![]() ![]() Strain: 168 / Gene: rpsC, BSU01220 Production host: ![]() ![]() References: UniProt: P21465 |
#33: Protein | Mass: 22250.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsD, BSU29660 Production host: ![]() ![]() References: UniProt: P21466 |
#34: Protein | Mass: 17362.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsE, spcA, BSU01330 Production host: ![]() ![]() References: UniProt: P21467 |
#35: Protein | Mass: 10723.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsF, BSU40910 Production host: ![]() ![]() References: UniProt: P21468 |
#36: Protein | Mass: 16885.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsG, BSU01110 Production host: ![]() ![]() References: UniProt: P21469 |
#37: Protein | Mass: 14770.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsH, BSU01300 Production host: ![]() ![]() References: UniProt: P12879 |
#38: Protein | Mass: 13748.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsI, BSU01500 Production host: ![]() ![]() References: UniProt: P21470 |
#39: Protein | Mass: 10856.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsJ, tetA, BSU01150 Production host: ![]() ![]() References: UniProt: P21471 |
#40: Protein | Mass: 11946.558 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsK, BSU01420 Production host: ![]() ![]() References: UniProt: P04969 |
#41: Protein | Mass: 14988.358 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsL, fun, strA, BSU01100 Production host: ![]() ![]() References: UniProt: P21472 |
#42: Protein | Mass: 12374.300 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsM, BSU01410 Production host: ![]() ![]() References: UniProt: P20282 |
#43: Protein | Mass: 7132.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsN1, rpsN, rpsNA, rpsZ, BSU01290 Production host: ![]() ![]() References: UniProt: P12878 |
#44: Protein | Mass: 10124.599 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsO, BSU16680 Production host: ![]() ![]() References: UniProt: P21473 |
#45: Protein | Mass: 9893.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsP, BSU15990 Production host: ![]() ![]() References: UniProt: P21474 |
#46: Protein | Mass: 9863.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsQ, BSU01250 Production host: ![]() ![]() References: UniProt: P12874 |
#47: Protein | Mass: 7387.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsR, BSU40890 Production host: ![]() ![]() References: UniProt: P21475 |
#48: Protein | Mass: 8990.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsS, BSU01200 Production host: ![]() ![]() References: UniProt: P21476 |
#49: Protein | Mass: 9121.647 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: rpsT, yqeO, BSU25550 Production host: ![]() ![]() 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.) ![]() ![]() Strain: 168 / Gene: relA, BSU27600 Production host: ![]() ![]() 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 |
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Sample preparation
Component | Name: Bacillus subtilis subsp. subtilis str. 168 / Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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 |
Image recording | Electron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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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 |