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Yorodumi- PDB-7o5b: Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-na... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o5b | ||||||
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Title | Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP bound | ||||||
Components |
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Keywords | RIBOSOME / signal recognition particle co-translational targeting alarmones translation GTPases stress response | ||||||
Function / homology | Function and homology information signal recognition particle / signal-recognition-particle GTPase / positive regulation of rRNA processing / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / nucleoid / rRNA processing / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...signal recognition particle / signal-recognition-particle GTPase / positive regulation of rRNA processing / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / nucleoid / rRNA processing / large ribosomal subunit / 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 / GTPase activity / mRNA binding / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å | ||||||
Authors | Kratzat, H. / Czech, L. / Berninghausen, O. / Bange, G. / Beckmann, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp. Authors: Laura Czech / Christopher-Nils Mais / Hanna Kratzat / Pinku Sarmah / Pietro Giammarinaro / Sven-Andreas Freibert / Hanna Folke Esser / Joanna Musial / Otto Berninghausen / Wieland Steinchen ...Authors: Laura Czech / Christopher-Nils Mais / Hanna Kratzat / Pinku Sarmah / Pietro Giammarinaro / Sven-Andreas Freibert / Hanna Folke Esser / Joanna Musial / Otto Berninghausen / Wieland Steinchen / Roland Beckmann / Hans-Georg Koch / Gert Bange / Abstract: The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known ...The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known as (p)ppGpp. Here, we report that (p)ppGpp inhibits the signal recognition particle (SRP)-dependent protein targeting pathway, which is essential for membrane protein biogenesis and protein secretion. More specifically, (p)ppGpp binds to the SRP GTPases Ffh and FtsY, and inhibits the formation of the SRP receptor-targeting complex, which is central for the coordinated binding of the translating ribosome to the SecYEG translocon. Cryo-EM analysis of SRP bound to translating ribosomes suggests that (p)ppGpp may induce a distinct conformational stabilization of the NG domain of Ffh and FtsY in Bacillus subtilis but not in E. coli. | ||||||
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 | 7o5b.cif.gz | 3.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7o5b.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7o5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o5b_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7o5b_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7o5b_validation.xml.gz | 180.6 KB | Display | |
Data in CIF | 7o5b_validation.cif.gz | 304.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/7o5b ftp://data.pdbj.org/pub/pdb/validation_reports/o5/7o5b | HTTPS FTP |
-Related structure data
Related structure data | 12734MC 7o9fC 7o9gC 7o9hC 7o9iC 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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1 |
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-Components
-RNA chain , 6 types, 6 molecules UVWXYA
#1: RNA chain | Mass: 24815.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 1837880844 |
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#2: RNA chain | Mass: 2612.665 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
#3: RNA chain | Mass: 85909.688 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 1837880844 |
#8: RNA chain | Mass: 936486.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 1491848961 |
#9: RNA chain | Mass: 36157.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 1150402534 |
#37: RNA chain | Mass: 496854.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 225184640 |
-Protein , 2 types, 2 molecules gh
#4: Protein | Mass: 49739.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: ffh, BSU15980 / Production host: Escherichia coli (E. coli) / References: UniProt: P37105 |
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#5: Protein | Mass: 10874.593 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
+50S ribosomal protein ... , 29 types, 29 molecules pqZabcdefijklmnorstuvwx012346
-30S ribosomal protein ... , 19 types, 19 molecules BCDEFGHIJKLMNOPQRST
#38: Protein | Mass: 28009.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21464 |
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#39: Protein | Mass: 24351.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21465 |
#40: Protein | Mass: 22874.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21466 |
#41: Protein | Mass: 17650.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21467 |
#42: Protein | Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21468 |
#43: Protein | Mass: 17915.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21469 |
#44: Protein | Mass: 14901.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12879 |
#45: Protein | Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21470 |
#46: Protein | Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21471 |
#47: Protein | Mass: 13993.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P04969 |
#48: Protein | Mass: 15248.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21472 |
#49: Protein | Mass: 13818.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P20282 |
#50: Protein | Mass: 7263.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12878 |
#51: Protein | Mass: 10597.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21473 |
#52: Protein | Mass: 10153.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21474 |
#53: Protein | Mass: 10220.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12874 |
#54: Protein | Mass: 8990.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21475 |
#55: Protein | Mass: 10607.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21476 |
#56: Protein | Mass: 9622.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21477 |
-Non-polymers , 1 types, 1 molecules
#57: Chemical | ChemComp-G4P / |
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-Details
Has ligand of interest | N |
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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: SRP-bound MifM-stalled ribosome nascent chain complex / Type: RIBOSOME / Entity ID: #1-#56 / Source: MULTIPLE SOURCES |
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Buffer solution | pH: 7.5 |
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: 25 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21229 / Symmetry type: POINT |