+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11862 | |||||||||
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Title | Structure of the bacterial RQC complex (Decoding State) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RIBOSOME / rqch / rqc / rqc2 / hsp15 / fibronectin-binding protein / NEMF / ribosome-associated quality control / ribosome-associated / 50s / Alanine-tailing | |||||||||
Function / homology | Function and homology information RQC complex / positive regulation of rRNA processing / nucleoid / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding ...RQC complex / positive regulation of rRNA processing / nucleoid / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / 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 / DNA binding / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) / Bacillus subtilis (strain 168) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
Authors | Filbeck S / Pfeffer S | |||||||||
Funding support | Germany, United States, 2 items
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Citation | Journal: Mol Cell / Year: 2021 Title: Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC. Authors: Sebastian Filbeck / Federico Cerullo / Helge Paternoga / George Tsaprailis / Claudio A P Joazeiro / Stefan Pfeffer / Abstract: Aborted translation produces large ribosomal subunits obstructed with tRNA-linked nascent chains, which are substrates of ribosome-associated quality control (RQC). Bacterial RqcH, a widely conserved ...Aborted translation produces large ribosomal subunits obstructed with tRNA-linked nascent chains, which are substrates of ribosome-associated quality control (RQC). Bacterial RqcH, a widely conserved RQC factor, senses the obstruction and recruits tRNA to modify nascent-chain C termini with a polyalanine degron. However, how RqcH and its eukaryotic homologs (Rqc2 and NEMF), despite their relatively simple architecture, synthesize such C-terminal tails in the absence of a small ribosomal subunit and mRNA has remained unknown. Here, we present cryoelectron microscopy (cryo-EM) structures of Bacillus subtilis RQC complexes representing different Ala tail synthesis steps. The structures explain how tRNA is selected via anticodon reading during recruitment to the A-site and uncover striking hinge-like movements in RqcH leading tRNA into a hybrid A/P-state associated with peptidyl-transfer. Finally, we provide structural, biochemical, and molecular genetic evidence identifying the Hsp15 homolog (encoded by rqcP) as a novel RQC component that completes the cycle by stabilizing the P-site tRNA conformation. Ala tailing thus follows mechanistic principles surprisingly similar to canonical translation elongation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11862.map.gz | 7.6 MB | EMDB map data format | |
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Header (meta data) | emd-11862-v30.xml emd-11862.xml | 46.5 KB 46.5 KB | Display Display | EMDB header |
Images | emd_11862.png | 169.2 KB | ||
Filedesc metadata | emd-11862.cif.gz | 10.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11862 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11862 | HTTPS FTP |
-Validation report
Summary document | emd_11862_validation.pdf.gz | 419 KB | Display | EMDB validaton report |
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Full document | emd_11862_full_validation.pdf.gz | 418.6 KB | Display | |
Data in XML | emd_11862_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_11862_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11862 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11862 | HTTPS FTP |
-Related structure data
Related structure data | 7aqcMC 7aqdC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11862.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Bacterial RQC complex
+Supramolecule #1: Bacterial RQC complex
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #15: Ala-tRNA (P-site)
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L6
+Macromolecule #8: 50S ribosomal protein L11
+Macromolecule #9: 50S ribosomal protein L13
+Macromolecule #10: 50S ribosomal protein L14
+Macromolecule #11: 50S ribosomal protein L15
+Macromolecule #12: 50S ribosomal protein L16
+Macromolecule #13: 50S ribosomal protein L17
+Macromolecule #14: 50S ribosomal protein L18
+Macromolecule #16: 50S ribosomal protein L20
+Macromolecule #17: Rqc2 homolog RqcH
+Macromolecule #18: 50S ribosomal protein L22
+Macromolecule #19: 50S ribosomal protein L24
+Macromolecule #20: 50S ribosomal protein L27
+Macromolecule #21: nascent polyalanine
+Macromolecule #22: 50S ribosomal protein L28
+Macromolecule #23: Uncharacterized protein YabO
+Macromolecule #24: 50S ribosomal protein L30
+Macromolecule #25: 50S ribosomal protein L19
+Macromolecule #26: 50S ribosomal protein L32
+Macromolecule #27: 50S ribosomal protein L33 1
+Macromolecule #28: 50S ribosomal protein L34
+Macromolecule #29: 50S ribosomal protein L35
+Macromolecule #30: 50S ribosomal protein L36
+Macromolecule #31: 50S ribosomal protein L21
+Macromolecule #32: 50S ribosomal protein L23
+Macromolecule #33: 50S ribosomal protein L29
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Output model | PDB-7aqc: |