+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30431 | |||||||||
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Title | ycbZ-stalled 70S ribosome | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information mRNA 5'-UTR binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / transferase activity ...mRNA 5'-UTR binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli 2362-75 (bacteria) / Escherichia coli 113303 (bacteria) / Escherichia coli H420 (bacteria) / Escherichia coli (strain K12) (bacteria) / Escherichia coli 907713 (bacteria) / Escherichia coli UMEA 3718-1 (bacteria) / Escherichia coli 2.3916 (bacteria) / Escherichia coli KTE112 (bacteria) / Escherichia coli 4.0522 (bacteria) / Escherichia coli O7:K1 (strain IAI39 / ExPEC) (bacteria) / Escherichia coli O26:H11 (bacteria) / Escherichia coli KTE73 (bacteria) / Escherichia coli MS 198-1 (bacteria) / Escherichia coli MS 117-3 (bacteria) / Escherichia coli HVH 87 (4-5977630) (bacteria) / Escherichia coli M863 (bacteria) / Escherichia coli 2-427-07_S4_C3 (bacteria) / Escherichia coli KTE64 (bacteria) / Escherichia coli O121:H19 (bacteria) / Escherichia coli TA054 (bacteria) / Escherichia coli DEC1D (bacteria) / Escherichia coli 3-373-03_S4_C2 (bacteria) / Escherichia coli 99.0741 (bacteria) / Escherichia coli KTE75 (bacteria) / Escherichia coli O177 (bacteria) / Escherichia coli MS 84-1 (bacteria) / Escherichia coli G3/10 (bacteria) / Escherichia coli H461 (bacteria) / Escherichia coli 908573 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Yokoyama T / Shirouzu M / Ito T | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: RNA / Year: 2022 Title: The landscape of translational stall sites in bacteria revealed by monosome and disome profiling. Authors: Tomoya Fujita / Takeshi Yokoyama / Mikako Shirouzu / Hideki Taguchi / Takuhiro Ito / Shintaro Iwasaki / Abstract: Ribosome pauses are associated with various cotranslational events and determine the fate of mRNAs and proteins. Thus, the identification of precise pause sites across the transcriptome is desirable; ...Ribosome pauses are associated with various cotranslational events and determine the fate of mRNAs and proteins. Thus, the identification of precise pause sites across the transcriptome is desirable; however, the landscape of ribosome pauses in bacteria remains ambiguous. Here, we harness monosome and disome (or collided ribosome) profiling strategies to survey ribosome pause sites in Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences: a low frequency of disomes at stop codons, collisions occurring immediately after 70S assembly on start codons, and shorter queues of ribosomes trailing upstream. The pause sites corresponded with the biochemical validation by integrated nascent chain profiling (iNP) to detect polypeptidyl-tRNA, an elongation intermediate. Moreover, the subset of those sites showed puromycin resistance, presenting slow peptidyl transfer. Among the identified sites, the ribosome pause at Asn586 of was validated by biochemical reporter assay, tRNA sequencing (tRNA-seq), and cryo-electron microscopy (cryo-EM) experiments. Our results provide a useful resource for ribosome stalling sites in bacteria. | |||||||||
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_30431.map.gz | 96.4 MB | EMDB map data format | |
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Header (meta data) | emd-30431-v30.xml emd-30431.xml | 63.8 KB 63.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30431_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_30431.png | 89.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30431 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30431 | HTTPS FTP |
-Related structure data
Related structure data | 7cpjMC 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_30431.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.47 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 : ribosome
+Supramolecule #1: ribosome
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #22: 23S ribosomal RNA
+Macromolecule #23: 5S ribosomal RNA
+Macromolecule #55: P/P tRNA
+Macromolecule #56: mRNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #24: 50S ribosomal protein L2
+Macromolecule #25: 50S ribosomal protein L3
+Macromolecule #26: 50S ribosomal protein L4
+Macromolecule #27: 50S ribosomal protein L5
+Macromolecule #28: 50S ribosomal protein L6
+Macromolecule #29: 50S ribosomal protein L9
+Macromolecule #30: 50S ribosomal protein L11
+Macromolecule #31: 50S ribosomal protein L13
+Macromolecule #32: 50S ribosomal protein L14
+Macromolecule #33: 50S ribosomal protein L15
+Macromolecule #34: 50S ribosomal protein L16
+Macromolecule #35: 50S ribosomal protein L17
+Macromolecule #36: 50S ribosomal protein L18
+Macromolecule #37: 50S ribosomal protein L19
+Macromolecule #38: 50S ribosomal protein L20
+Macromolecule #39: 50S ribosomal protein L21
+Macromolecule #40: 50S ribosomal protein L22
+Macromolecule #41: 50S ribosomal protein L23
+Macromolecule #42: 50S ribosomal protein L24
+Macromolecule #43: 50S ribosomal protein L25
+Macromolecule #44: 50S ribosomal protein L27
+Macromolecule #45: 50S ribosomal protein L28
+Macromolecule #46: 50S ribosomal protein L29
+Macromolecule #47: 50S ribosomal protein L30
+Macromolecule #48: 50S ribosomal protein L32
+Macromolecule #49: 50S ribosomal protein L33
+Macromolecule #50: 50S ribosomal protein L34
+Macromolecule #51: 50S ribosomal protein L35
+Macromolecule #52: 50S ribosomal protein L36
+Macromolecule #53: 50S ribosomal protein L10
+Macromolecule #54: 50S ribosomal protein L31
+Macromolecule #57: ISOLEUCINE
+Macromolecule #58: PROLINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Sugar embedding | Material: amorphous ice |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 23500 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-7cpj: |