+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9242 | |||||||||
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Title | Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state) | |||||||||
Map data | Postprocessed map | |||||||||
Sample |
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Function / homology | Function and homology information Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Translation initiation complex formation / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Translation initiation complex formation / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / : / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Separation of Sister Chromatids / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of endodeoxyribonuclease activity / : / negative regulation of DNA repair / TORC2 complex binding / oxidized purine DNA binding / supercoiled DNA binding / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein kinase A binding / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / SARS-CoV-1 modulates host translation machinery / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Peptide chain elongation / Selenocysteine synthesis / protein-RNA complex assembly / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / organelle membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rough endoplasmic reticulum / spindle assembly / MDM2/MDM4 family protein binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation initiation factor binding / maturation of SSU-rRNA / : / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of apoptotic signaling pathway / positive regulation of microtubule polymerization / positive regulation of JUN kinase activity / negative regulation of protein ubiquitination / Hsp70 protein binding / positive regulation of interleukin-2 production / DNA-(apurinic or apyrimidinic site) lyase Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) / Bovine (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Brown A / Baird MR / Yip MCJ / Murray J / Shao S | |||||||||
Citation | Journal: Elife / Year: 2018 Title: Structures of translationally inactive mammalian ribosomes. Authors: Alan Brown / Matthew R Baird / Matthew Cj Yip / Jason Murray / Sichen Shao / Abstract: The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. ...The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression. | |||||||||
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_9242.map.gz | 12.8 MB | EMDB map data format | |
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Header (meta data) | emd-9242-v30.xml emd-9242.xml | 97.6 KB 97.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9242_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_9242.png | 172 KB | ||
Others | emd_9242_additional.map.gz emd_9242_half_map_1.map.gz emd_9242_half_map_2.map.gz | 214.2 MB 214.5 MB 214.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9242 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9242 | HTTPS FTP |
-Related structure data
Related structure data | 6mteMC 9234C 9235C 9236C 9237C 9239C 9240C 9241C 6mtbC 6mtcC 6mtdC C: citing same article (ref.) M: atomic model generated by this map |
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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_9242.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Pre-postprocessed map
File | emd_9242_additional.map | ||||||||||||
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Annotation | Pre-postprocessed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_9242_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_9242_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)
+Supramolecule #1: Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)
+Macromolecule #1: 28S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #50: 18S rRNA
+Macromolecule #4: uL2
+Macromolecule #5: uL3
+Macromolecule #6: uL4
+Macromolecule #7: uL18
+Macromolecule #8: eL6
+Macromolecule #9: uL30
+Macromolecule #10: eL8
+Macromolecule #11: uL6
+Macromolecule #12: uL16
+Macromolecule #13: uL5
+Macromolecule #14: eL13
+Macromolecule #15: eL14
+Macromolecule #16: eL15
+Macromolecule #17: uL13
+Macromolecule #18: uL22
+Macromolecule #19: eL18
+Macromolecule #20: eL19
+Macromolecule #21: eL20
+Macromolecule #22: eL21
+Macromolecule #23: eL22
+Macromolecule #24: uL14
+Macromolecule #25: eL24
+Macromolecule #26: uL23
+Macromolecule #27: uL24
+Macromolecule #28: eL27
+Macromolecule #29: uL15
+Macromolecule #30: eL29
+Macromolecule #31: eL30
+Macromolecule #32: eL31
+Macromolecule #33: eL32
+Macromolecule #34: eL33
+Macromolecule #35: eL34
+Macromolecule #36: uL29
+Macromolecule #37: eL36
+Macromolecule #38: eL37
+Macromolecule #39: eL38
+Macromolecule #40: eL39
+Macromolecule #41: eL40
+Macromolecule #42: eL41
+Macromolecule #43: eL42
+Macromolecule #44: eL43
+Macromolecule #45: eL28
+Macromolecule #46: uL10
+Macromolecule #47: uL11
+Macromolecule #48: eEF2
+Macromolecule #49: SERBP1
+Macromolecule #51: uS2
+Macromolecule #52: eS1
+Macromolecule #53: uS5
+Macromolecule #54: uS3
+Macromolecule #55: eS4
+Macromolecule #56: uS7
+Macromolecule #57: eS6
+Macromolecule #58: eS7
+Macromolecule #59: eS8
+Macromolecule #60: uS4
+Macromolecule #61: eS10
+Macromolecule #62: uS17
+Macromolecule #63: eS12
+Macromolecule #64: uS15
+Macromolecule #65: uS11
+Macromolecule #66: uS19
+Macromolecule #67: uS9
+Macromolecule #68: eS17
+Macromolecule #69: uS13
+Macromolecule #70: eS19
+Macromolecule #71: uS10
+Macromolecule #72: eS21
+Macromolecule #73: uS8
+Macromolecule #74: uS12
+Macromolecule #75: eS24
+Macromolecule #76: eS25
+Macromolecule #77: eS26
+Macromolecule #78: eS27
+Macromolecule #79: eS28
+Macromolecule #80: uS14
+Macromolecule #81: eS30
+Macromolecule #82: eS31
+Macromolecule #83: RACK1
+Macromolecule #84: MAGNESIUM ION
+Macromolecule #85: ZINC ION
+Macromolecule #86: GUANOSINE-5'-DIPHOSPHATE
-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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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-17 / Average exposure time: 1.1 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |