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Yorodumi- EMDB-0197: Multi-body refined map of the rabbit 80S collided with a stalled 80S -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0197 | |||||||||||||||
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Title | Multi-body refined map of the rabbit 80S collided with a stalled 80S | |||||||||||||||
Map data | Multi-body refined rabbit 80S ribosome collided with the stalled 80S ribosome | |||||||||||||||
Sample |
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Function / homology | Function and homology information maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / 5S rRNA binding / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / nucleolus ...maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / 5S rRNA binding / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / nucleolus / RNA binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||||||||
Authors | Juszkiewicz S / Chandrasekaran V / Lin Z / Kraatz S / Ramakrishnan V / Hegde RS | |||||||||||||||
Funding support | United Kingdom, France, 4 items
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Citation | Journal: Mol Cell / Year: 2018 Title: ZNF598 Is a Quality Control Sensor of Collided Ribosomes. Authors: Szymon Juszkiewicz / Viswanathan Chandrasekaran / Zhewang Lin / Sebastian Kraatz / V Ramakrishnan / Ramanujan S Hegde / Abstract: Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates ...Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status. | |||||||||||||||
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_0197.map.gz | 23.7 MB | EMDB map data format | |
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Header (meta data) | emd-0197-v30.xml emd-0197.xml | 94.9 KB 94.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0197_fsc.xml | 17.6 KB | Display | FSC data file |
Images | emd_0197.png | 157.7 KB | ||
Masks | emd_0197_msk_1.map | 476.8 MB | Mask map | |
Others | emd_0197_half_map_1.map.gz emd_0197_half_map_2.map.gz | 325.9 MB 324.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0197 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0197 | HTTPS FTP |
-Related structure data
Related structure data | 6hcqMC 0192C 0194C 0195C 6hcfC 6hcjC 6hcmC 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_0197.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Multi-body refined rabbit 80S ribosome collided with the stalled 80S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_0197_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Body2 half1 map
File | emd_0197_half_map_1.map | ||||||||||||
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Annotation | Body2 half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Body2 half1 map
File | emd_0197_half_map_2.map | ||||||||||||
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Annotation | Body2 half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Rabbit 80S on globin mRNA in the rotated state with A/P and P/E tRNAs
+Supramolecule #1: Rabbit 80S on globin mRNA in the rotated state with A/P and P/E tRNAs
+Macromolecule #1: 28S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #4: 18S ribosomal RNA
+Macromolecule #79: A/P tRNA
+Macromolecule #82: mRNA
+Macromolecule #83: P/E tRNA
+Macromolecule #5: uS2
+Macromolecule #6: 40S ribosomal protein S3a
+Macromolecule #7: eS1
+Macromolecule #8: uS3
+Macromolecule #9: eS4
+Macromolecule #10: Ribosomal protein S5
+Macromolecule #11: 40S ribosomal protein S6
+Macromolecule #12: 40S ribosomal protein S7
+Macromolecule #13: eS8
+Macromolecule #14: Ribosomal protein S9 (Predicted)
+Macromolecule #15: eS10
+Macromolecule #16: Ribosomal protein S11
+Macromolecule #17: 40S ribosomal protein S12
+Macromolecule #18: uS15
+Macromolecule #19: uS11
+Macromolecule #20: uS19
+Macromolecule #21: Ribosomal protein S16
+Macromolecule #22: eS17
+Macromolecule #23: uS13
+Macromolecule #24: eS19
+Macromolecule #25: uS10
+Macromolecule #26: eS21
+Macromolecule #27: Ribosomal protein S15a
+Macromolecule #28: uS12
+Macromolecule #29: eS24
+Macromolecule #30: eS25
+Macromolecule #31: eS26
+Macromolecule #32: 40S ribosomal protein S27
+Macromolecule #33: Ribosomal protein S28
+Macromolecule #34: uS14
+Macromolecule #35: 40S ribosomal protein S30
+Macromolecule #36: Ribosomal protein S27a
+Macromolecule #37: RACK1
+Macromolecule #38: Ribosomal protein L8
+Macromolecule #39: uL3
+Macromolecule #40: uL4
+Macromolecule #41: 60S ribosomal protein L5
+Macromolecule #42: 60S ribosomal protein L6
+Macromolecule #43: uL30
+Macromolecule #44: eL8
+Macromolecule #45: uL6
+Macromolecule #46: 60S ribosomal protein L10
+Macromolecule #47: Ribosomal protein L11
+Macromolecule #48: eL13
+Macromolecule #49: Ribosomal protein L14
+Macromolecule #50: Ribosomal protein L15
+Macromolecule #51: uL13
+Macromolecule #52: uL22
+Macromolecule #53: eL18
+Macromolecule #54: eL19
+Macromolecule #55: eL20
+Macromolecule #56: eL21
+Macromolecule #57: eL22
+Macromolecule #58: Ribosomal protein L23
+Macromolecule #59: uL23
+Macromolecule #60: Ribosomal protein L26
+Macromolecule #61: 60S ribosomal protein L27
+Macromolecule #62: uL15
+Macromolecule #63: eL29
+Macromolecule #64: eL30
+Macromolecule #65: eL31
+Macromolecule #66: eL32
+Macromolecule #67: eL33
+Macromolecule #68: eL34
+Macromolecule #69: uL29
+Macromolecule #70: 60S ribosomal protein L36
+Macromolecule #71: Ribosomal protein L37
+Macromolecule #72: eL38
+Macromolecule #73: eL39
+Macromolecule #74: eL40
+Macromolecule #75: eL41
+Macromolecule #76: eL42
+Macromolecule #77: eL43
+Macromolecule #78: eL28
+Macromolecule #80: uL10
+Macromolecule #81: Ribosomal protein L12
+Macromolecule #84: Ribosomal protein
+Macromolecule #85: nascent chain
+Macromolecule #86: MAGNESIUM ION
+Macromolecule #87: ZINC ION
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 1.79 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |