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- EMDB-0195: Multi-body refined map of the rabbit 80S stalled on globin mRNA a... -
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Basic information
Entry | Database: EMDB / ID: EMD-0195 | |||||||||||||||
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Title | Multi-body refined map of the rabbit 80S stalled on globin mRNA at the stop codon | |||||||||||||||
![]() | Multi-body refined rabbit 80S ribosome stalled on globin mRNA at the stop codon | |||||||||||||||
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![]() | Translation / Quality Control / Ribosome | |||||||||||||||
Function / homology | ![]() ribosomal subunit / exit from mitosis / optic nerve development / retinal ganglion cell axon guidance / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / 90S preribosome / ribosomal small subunit export from nucleus / translation regulator activity ...ribosomal subunit / exit from mitosis / optic nerve development / retinal ganglion cell axon guidance / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / 90S preribosome / ribosomal small subunit export from nucleus / translation regulator activity / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / spindle / mRNA 5'-UTR binding / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of canonical Wnt signaling pathway / rhythmic process / regulation of translation / large ribosomal subunit / ribosome binding / ribosomal small subunit assembly / ribosomal small subunit biogenesis / retina development in camera-type eye / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / defense response to Gram-negative bacterium / perikaryon / cytosolic large ribosomal subunit / killing of cells of another organism / cytoplasmic translation / tRNA binding / cell differentiation / mitochondrial inner membrane / postsynaptic density / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / centrosome / apoptotic process / dendrite / synapse / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||||||||
![]() | Juszkiewicz S / Chandrasekaran V | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 23.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 103.3 KB 103.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.6 KB | Display | ![]() |
Images | ![]() | 157.7 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Filedesc metadata | ![]() | 20.7 KB | ||
Others | ![]() ![]() | 345.1 MB 345.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 407.9 KB | Display | ![]() |
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Full document | ![]() | 407 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hcmMC ![]() 0192C ![]() 0194C ![]() 0197C ![]() 6hcfC ![]() 6hcjC ![]() 6hcqC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Multi-body refined rabbit 80S ribosome stalled on globin mRNA at the stop codon | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Body1 half2 map
File | emd_0195_half_map_1.map | ||||||||||||
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Annotation | Body1 half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Body1 half1 map
File | emd_0195_half_map_2.map | ||||||||||||
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Annotation | Body1 half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Rabbit 80S stalled on globin mRNA at the stop codon
+Supramolecule #1: Rabbit 80S stalled on globin mRNA at the stop codon
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #37: 28S ribosomal RNA
+Macromolecule #38: 5S ribosomal RNA
+Macromolecule #39: 5.8S ribosomal RNA
+Macromolecule #80: P-site tRNA
+Macromolecule #81: mRNA
+Macromolecule #2: uS2
+Macromolecule #3: 40S ribosomal protein S3a
+Macromolecule #4: uS5
+Macromolecule #5: uS3
+Macromolecule #6: eS4
+Macromolecule #7: Ribosomal protein S5
+Macromolecule #8: 40S ribosomal protein S6
+Macromolecule #9: 40S ribosomal protein S7
+Macromolecule #10: eS8
+Macromolecule #11: Ribosomal protein S9 (Predicted)
+Macromolecule #12: eS10
+Macromolecule #13: Ribosomal protein S11
+Macromolecule #14: 40S ribosomal protein S12
+Macromolecule #15: uS15
+Macromolecule #16: uS11
+Macromolecule #17: uS19
+Macromolecule #18: Ribosomal protein S16
+Macromolecule #19: eS17
+Macromolecule #20: uS13
+Macromolecule #21: eS19
+Macromolecule #22: uS10
+Macromolecule #23: eS21
+Macromolecule #24: Ribosomal protein S15a
+Macromolecule #25: uS12
+Macromolecule #26: eS24
+Macromolecule #27: eS25
+Macromolecule #28: eS26
+Macromolecule #29: 40S ribosomal protein S27
+Macromolecule #30: Ribosomal protein S28
+Macromolecule #31: uS14
+Macromolecule #32: 40S ribosomal protein S30
+Macromolecule #33: Ribosomal protein S27a
+Macromolecule #34: RACK1
+Macromolecule #35: eRF1(AAQ)
+Macromolecule #36: ATP binding cassette subfamily E member 1
+Macromolecule #40: Ribosomal protein L8
+Macromolecule #41: uL3
+Macromolecule #42: uL4
+Macromolecule #43: 60S ribosomal protein L6
+Macromolecule #44: uL30
+Macromolecule #45: uL6
+Macromolecule #46: eL13
+Macromolecule #47: Ribosomal protein L14
+Macromolecule #48: Ribosomal protein L15
+Macromolecule #49: uL13
+Macromolecule #50: uL22
+Macromolecule #51: eL18
+Macromolecule #52: eL19
+Macromolecule #53: eL20
+Macromolecule #54: eL21
+Macromolecule #55: eL22
+Macromolecule #56: Ribosomal protein L23
+Macromolecule #57: eL24
+Macromolecule #58: uL23
+Macromolecule #59: Ribosomal protein L26
+Macromolecule #60: eL27
+Macromolecule #61: uL15
+Macromolecule #62: eL29
+Macromolecule #63: eL30
+Macromolecule #64: eL31
+Macromolecule #65: eL32
+Macromolecule #66: eL33
+Macromolecule #67: eL34
+Macromolecule #68: uL29
+Macromolecule #69: 60S ribosomal protein L36
+Macromolecule #70: Ribosomal protein L37
+Macromolecule #71: eL38
+Macromolecule #72: eL39
+Macromolecule #73: eL40
+Macromolecule #74: eL41
+Macromolecule #75: eL42
+Macromolecule #76: eL43
+Macromolecule #77: eL28
+Macromolecule #78: uL10
+Macromolecule #79: Ribosomal protein L12
+Macromolecule #82: Ribosomal protein L11
+Macromolecule #83: eL8
+Macromolecule #84: 60S ribosomal protein L5
+Macromolecule #85: 60S ribosomal protein L10
+Macromolecule #86: nascent chain
+Macromolecule #87: Ribosomal protein
+Macromolecule #88: MAGNESIUM ION
+Macromolecule #89: ZINC ION
+Macromolecule #90: IRON/SULFUR CLUSTER
+Macromolecule #91: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.79 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |