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Yorodumi- EMDB-0195: Multi-body refined map of the rabbit 80S stalled on globin mRNA a... -
+Open data
-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 | |||||||||||||||
Map data | Multi-body refined rabbit 80S ribosome stalled on globin mRNA at the stop codon | |||||||||||||||
Sample |
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Keywords | Translation / Quality Control / Ribosome | |||||||||||||||
Function / homology | Function and homology information regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition ...regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / ribosomal small subunit binding / 90S preribosome / TOR signaling / T cell proliferation involved in immune response / erythrocyte development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translational termination / translation regulator activity / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / maturation of LSU-rRNA / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / small-subunit processome / positive regulation of translation / translational initiation / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / spindle / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / small ribosomal subunit rRNA binding / positive regulation of canonical Wnt signaling pathway / rhythmic process / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / retina development in camera-type eye / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit / T cell differentiation in thymus / cell body / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / perikaryon / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / tRNA binding / mitochondrial inner membrane / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / iron ion binding / positive regulation of apoptotic process / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / cell division / DNA repair / mRNA binding / centrosome / ubiquitin protein ligase binding / dendrite / positive regulation of cell population proliferation / synapse / positive regulation of gene expression Similarity search - Function | |||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||||||||
Authors | Juszkiewicz S / Chandrasekaran V | |||||||||||||||
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_0195.map.gz | 23.3 MB | EMDB map data format | |
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Header (meta data) | emd-0195-v30.xml emd-0195.xml | 103.3 KB 103.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0195_fsc.xml | 17.6 KB | Display | FSC data file |
Images | emd_0195.png | 157.7 KB | ||
Masks | emd_0195_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-0195.cif.gz | 20.7 KB | ||
Others | emd_0195_half_map_1.map.gz emd_0195_half_map_2.map.gz | 345.1 MB 345.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0195 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0195 | HTTPS FTP |
-Validation report
Summary document | emd_0195_validation.pdf.gz | 407.9 KB | Display | EMDB validaton report |
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Full document | emd_0195_full_validation.pdf.gz | 407 KB | Display | |
Data in XML | emd_0195_validation.xml.gz | 22.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0195 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0195 | 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 (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_0195.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 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 | emd_0195_msk_1.map | ||||||||||||
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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 |
-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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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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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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |