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Open data
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Basic information
Entry | Database: PDB / ID: 7qv2 | ||||||
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Title | Bacillus subtilis collided disome (Collided 70S) | ||||||
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![]() | RIBOSOME / Collision / MutS2 / disome / RQC / ssra / ribosomal collision / mRNA endonuclease | ||||||
Function / homology | ![]() positive regulation of rRNA processing / 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 ...positive regulation of rRNA processing / 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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Filbeck, S. / Pfeffer, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue. Authors: Federico Cerullo / Sebastian Filbeck / Pratik Rajendra Patil / Hao-Chih Hung / Haifei Xu / Julia Vornberger / Florian W Hofer / Jaro Schmitt / Guenter Kramer / Bernd Bukau / Kay Hofmann / ...Authors: Federico Cerullo / Sebastian Filbeck / Pratik Rajendra Patil / Hao-Chih Hung / Haifei Xu / Julia Vornberger / Florian W Hofer / Jaro Schmitt / Guenter Kramer / Bernd Bukau / Kay Hofmann / Stefan Pfeffer / Claudio A P Joazeiro / ![]() ![]() Abstract: Ribosome stalling during translation is detrimental to cellular fitness, but how this is sensed and elicits recycling of ribosomal subunits and quality control of associated mRNA and incomplete ...Ribosome stalling during translation is detrimental to cellular fitness, but how this is sensed and elicits recycling of ribosomal subunits and quality control of associated mRNA and incomplete nascent chains is poorly understood. Here we uncover Bacillus subtilis MutS2, a member of the conserved MutS family of ATPases that function in DNA mismatch repair, as an unexpected ribosome-binding protein with an essential function in translational quality control. Cryo-electron microscopy analysis of affinity-purified native complexes shows that MutS2 functions in sensing collisions between stalled and translating ribosomes and suggests how ribosome collisions can serve as platforms to deploy downstream processes: MutS2 has an RNA endonuclease small MutS-related (SMR) domain, as well as an ATPase/clamp domain that is properly positioned to promote ribosomal subunit dissociation, which is a requirement both for ribosome recycling and for initiation of ribosome-associated protein quality control (RQC). Accordingly, MutS2 promotes nascent chain modification with alanine-tail degrons-an early step in RQC-in an ATPase domain-dependent manner. The relevance of these observations is underscored by evidence of strong co-occurrence of MutS2 and RQC genes across bacterial phyla. Overall, the findings demonstrate a deeply conserved role for ribosome collisions in mounting a complex response to the interruption of translation within open reading frames. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 181.6 KB | Display | |
Data in CIF | ![]() | 323.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 14158MC ![]() 7qv1C ![]() 7qv3C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
+50S ribosomal protein ... , 27 types, 27 molecules 012346CDEFGJKLMNOPQRSTUWYZu
-RNA chain , 6 types, 6 molecules ABHVax
#7: RNA chain | Mass: 9442.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
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#8: RNA chain | Mass: 36157.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 1150402534 |
#14: RNA chain | Mass: 24815.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 1837880844 |
#28: RNA chain | Mass: 949646.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 1491848961 |
#32: RNA chain | Mass: 500608.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 225184640 |
#53: RNA chain | Mass: 24486.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 1837880844 |
-Protein/peptide , 1 types, 1 molecules I
#15: Protein/peptide | Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
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-30S ribosomal protein ... , 19 types, 19 molecules bcdefghijklmnopqrst
#33: Protein | Mass: 28009.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21464 |
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#34: Protein | Mass: 24364.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21465 |
#35: Protein | Mass: 22874.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21466 |
#36: Protein | Mass: 17650.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21467 |
#37: Protein | Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21468 |
#38: Protein | Mass: 17915.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21469 |
#39: Protein | Mass: 14901.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P12879 |
#40: Protein | Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21470 |
#41: Protein | Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21471 |
#42: Protein | Mass: 13952.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P04969 |
#43: Protein | Mass: 15248.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21472 |
#44: Protein | Mass: 13818.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P20282 |
#45: Protein | Mass: 7263.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P12878 |
#46: Protein | Mass: 10597.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21473 |
#47: Protein | Mass: 10153.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21474 |
#48: Protein | Mass: 10220.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P12874 |
#49: Protein | Mass: 8990.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21475 |
#50: Protein | Mass: 10607.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21476 |
#51: Protein | Mass: 9622.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: 168 / References: UniProt: P21477 |
-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: Collided disome from Bacillus subtilis / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
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 / Nominal defocus max: 2000 nm / Nominal defocus min: 750 nm |
Image recording | Electron dose: 46.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 8297591 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27833 / Details: Local resolution ranging from 3.2 - 6.0 / Symmetry type: POINT |