+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10181 | ||||||||||||||||||
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Title | Rabbit 80S ribosome stalled on a poly(A) tail | ||||||||||||||||||
Map data | Structure of rabbit 80S stalled on a polyA tail | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information ribosomal subunit / regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / 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 / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein-DNA complex disassembly ...ribosomal subunit / regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / 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 / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / negative regulation of DNA repair / oxidized purine DNA binding / G1 to G0 transition / supercoiled DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / NF-kappaB complex / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / protein kinase A binding / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / ribosomal small subunit export from nucleus / translation regulator activity / cellular response to actinomycin D / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / rough endoplasmic reticulum / gastrulation / spindle assembly / signaling adaptor activity / MDM2/MDM4 family protein binding / : / rescue of stalled ribosome / negative regulation of smoothened signaling pathway / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of ubiquitin-dependent protein catabolic process / cytosolic ribosome / negative regulation of peptidyl-serine phosphorylation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / positive regulation of microtubule polymerization / ribosomal large subunit biogenesis / negative regulation of protein ubiquitination / Hsp70 protein binding / positive regulation of interleukin-2 production / cellular response to leukemia inhibitory factor / small-subunit processome / SH2 domain binding / cyclin binding / DNA endonuclease activity / positive regulation of translation / protein kinase C binding / : / cellular response to glucose stimulus / positive regulation of protein-containing complex assembly / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / base-excision repair / cellular response to gamma radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / cytoplasmic ribonucleoprotein granule / transcription coactivator binding / negative regulation of cell growth / positive regulation of non-canonical NF-kappaB signal transduction / mitotic spindle / small ribosomal subunit rRNA binding / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / cellular response to growth factor stimulus / ruffle membrane / rRNA processing / positive regulation of canonical Wnt signaling pathway / cytosolic small ribosomal subunit / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ribosome binding / large ribosomal subunit / cell body / 5S rRNA binding / cellular response to tumor necrosis factor / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / midbody / microtubule binding / protein phosphatase binding / mitochondrial inner membrane / DNA-binding transcription factor binding / negative regulation of translation / postsynaptic density Similarity search - Function | ||||||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) / Rabbit (rabbit) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||||||||
Authors | Chandrasekaran V / Juszkiewicz S / Choi J / Puglisi JD / Brown A / Shao S / Ramakrishnan V / Hegde RS | ||||||||||||||||||
Funding support | United Kingdom, United States, 5 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Mechanism of ribosome stalling during translation of a poly(A) tail. Authors: Viswanathan Chandrasekaran / Szymon Juszkiewicz / Junhong Choi / Joseph D Puglisi / Alan Brown / Sichen Shao / V Ramakrishnan / Ramanujan S Hegde / Abstract: Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. ...Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. The most common mRNA defect in eukaryotes is probably inappropriate polyadenylation at near-cognate sites within the coding region. How ribosomes stall selectively when they encounter poly(A) is unclear. Here, we use biochemical and structural approaches in mammalian systems to show that poly-lysine, encoded by poly(A), favors a peptidyl-transfer RNA conformation suboptimal for peptide bond formation. This conformation partially slows elongation, permitting poly(A) mRNA in the ribosome's decoding center to adopt a ribosomal RNA-stabilized single-stranded helix. The reconfigured decoding center clashes with incoming aminoacyl-tRNA, thereby precluding elongation. Thus, coincidence detection of poly-lysine in the exit tunnel and poly(A) in the decoding center allows ribosomes to detect aberrant mRNAs selectively, stall elongation and trigger downstream quality control pathways essential for cellular homeostasis. | ||||||||||||||||||
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_10181.map.gz | 63.5 MB | EMDB map data format | |
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Header (meta data) | emd-10181-v30.xml emd-10181.xml | 112.4 KB 112.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10181_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_10181.png | 271.8 KB | ||
Masks | emd_10181_msk_1.map | 512 MB | Mask map | |
Others | emd_10181_additional.map.gz emd_10181_half_map_1.map.gz emd_10181_half_map_2.map.gz | 411.2 MB 413.5 MB 413.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10181 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10181 | HTTPS FTP |
-Related structure data
Related structure data | 6sgcMC 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_10181.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of rabbit 80S stalled on a polyA tail | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.085 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_10181_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_10181_additional.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half1 map
File | emd_10181_half_map_1.map | ||||||||||||
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Annotation | Half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 map
File | emd_10181_half_map_2.map | ||||||||||||
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Annotation | Half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Rabbit 80S ribosome stalled on polyA mRNA
+Supramolecule #1: Rabbit 80S ribosome stalled on polyA mRNA
+Supramolecule #2: ribosome
+Supramolecule #3: polyA mRNA
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #35: polyA mRNA
+Macromolecule #80: 28S ribosomal RNA
+Macromolecule #81: 5S ribosomal RNA
+Macromolecule #82: 5.8S ribosomal RNA
+Macromolecule #85: tRNA (Lys3)
+Macromolecule #2: uS2
+Macromolecule #3: 40S ribosomal protein S3a
+Macromolecule #4: uS5
+Macromolecule #5: uS5
+Macromolecule #6: 40S ribosomal protein S4
+Macromolecule #7: Ribosomal protein S5
+Macromolecule #8: 40S ribosomal protein S6
+Macromolecule #9: 40S ribosomal protein S7
+Macromolecule #10: 40S ribosomal protein S8
+Macromolecule #11: Ribosomal protein S9 (Predicted)
+Macromolecule #12: S10_plectin domain-ontaining protein
+Macromolecule #13: Ribosomal protein S11
+Macromolecule #14: 40S ribosomal protein S12
+Macromolecule #15: Ribosomal_S13_N domain-containing protein
+Macromolecule #16: uS11
+Macromolecule #17: uS19
+Macromolecule #18: Ribosomal protein S16
+Macromolecule #19: eS17
+Macromolecule #20: eS13
+Macromolecule #21: eS19
+Macromolecule #22: Ribosomal_S10 domain-containing protein
+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: WD_REPEATS_REGION domain-containing protein
+Macromolecule #36: Ribosomal protein L8
+Macromolecule #37: uL3
+Macromolecule #38: uL4
+Macromolecule #39: 60S ribosomal protein L5
+Macromolecule #40: 60S ribosomal protein L6
+Macromolecule #41: uL30
+Macromolecule #42: eL8
+Macromolecule #43: uL6
+Macromolecule #44: 60S ribosomal protein L10
+Macromolecule #45: Ribosomal protein L11
+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: TRASH domain-containing protein
+Macromolecule #58: Ribosomal_L23eN domain-containing protein
+Macromolecule #59: Ribosomal protein L26
+Macromolecule #60: 60S ribosomal protein L27
+Macromolecule #61: Ribosomal_L18e/L15P domain-containing protein
+Macromolecule #62: eL29
+Macromolecule #63: Ribosomal_L7Ae domain-containing protein
+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: 60s ribosomal protein l41
+Macromolecule #75: eL42
+Macromolecule #76: eL43
+Macromolecule #77: Ribosomal_L28e domain-containing protein
+Macromolecule #78: uL10
+Macromolecule #79: Ribosomal protein L12
+Macromolecule #83: poly-lysine nascent chain
+Macromolecule #84: Ribosomal protein
+Macromolecule #86: MAGNESIUM ION
+Macromolecule #87: ZINC ION
+Macromolecule #88: SPERMIDINE
-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 | #0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Detector mode: INTEGRATING / #0 - Average electron dose: 41.8 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON III (4k x 4k) / #1 - Average electron dose: 41.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6sgc: |