+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14751 | |||||||||
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Title | Rabbit 80S ribosome as it decodes the Sec-UGA codon | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Selenocysteine / recoding / 80S / RIBOSOME | |||||||||
Function / homology | Function and homology information forebrain neuron development / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / selenocysteine incorporation / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / selenocysteine insertion sequence binding / L13a-mediated translational silencing of Ceruloplasmin expression ...forebrain neuron development / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / selenocysteine incorporation / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / selenocysteine insertion sequence binding / 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) / striatum development / ribosomal subunit / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / TOR signaling / mTORC1-mediated signalling / Peptide chain elongation / Selenocysteine synthesis / 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 / gastrulation / rough endoplasmic reticulum / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribonucleoprotein complex binding / translation elongation factor activity / Nuclear events stimulated by ALK signaling in cancer / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / DNA-(apurinic or apyrimidinic site) lyase / small-subunit processome / cytosolic ribosome / mRNA 3'-UTR binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosomal small subunit biogenesis / cytoplasmic ribonucleoprotein granule / rRNA processing / Regulation of expression of SLITs and ROBOs / cytosolic small ribosomal subunit / ribosome binding / large ribosomal subunit / glucose homeostasis / regulation of translation / heparin binding / cell body / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / SARS-CoV-2 modulates host translation machinery / tRNA binding / postsynaptic density / rRNA binding / ribosome / structural constituent of ribosome / cadherin binding / ribonucleoprotein complex / translation / positive regulation of apoptotic process / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / dendrite / synapse / positive regulation of cell population proliferation / GTP binding / nucleolus / protein kinase binding / endoplasmic reticulum / mitochondrion / DNA binding / RNA binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Cricket paralysis virus / Rattus norvegicus (Norway rat) / Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Hilal T / Simonovic M / Spahn CMT | |||||||||
Funding support | Germany, United States, 2 items
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Citation | Journal: Science / Year: 2022 Title: Structure of the mammalian ribosome as it decodes the selenocysteine UGA codon. Authors: Tarek Hilal / Benjamin Y Killam / Milica Grozdanović / Malgorzata Dobosz-Bartoszek / Justus Loerke / Jörg Bürger / Thorsten Mielke / Paul R Copeland / Miljan Simonović / Christian M T Spahn / Abstract: The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec ...The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec UGA recoding in mammals. A complex between the noncoding Sec-insertion sequence (SECIS), SECIS-binding protein 2 (SBP2), and 40 ribosomal subunit enables Sec-specific elongation factor eEFSec to deliver Sec. eEFSec and SBP2 do not interact directly but rather deploy their carboxyl-terminal domains to engage with the opposite ends of the SECIS. By using its Lys-rich and carboxyl-terminal segments, the ribosomal protein eS31 simultaneously interacts with Sec-specific transfer RNA (tRNA) and SBP2, which further stabilizes the assembly. eEFSec is indiscriminate toward l-serine and facilitates its misincorporation at Sec UGA codons. Our results support a fundamentally distinct mechanism of Sec UGA recoding in eukaryotes from that in bacteria. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14751.map.gz | 105.6 MB | EMDB map data format | |
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Header (meta data) | emd-14751-v30.xml emd-14751.xml | 130.1 KB 130.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14751_fsc.xml | 17.9 KB | Display | FSC data file |
Images | emd_14751.png | 127.6 KB | ||
Filedesc metadata | emd-14751.cif.gz | 24.7 KB | ||
Others | emd_14751_additional_1.map.gz emd_14751_half_map_1.map.gz emd_14751_half_map_2.map.gz | 105.6 MB 475.7 MB 475.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14751 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14751 | HTTPS FTP |
-Related structure data
Related structure data | 7zjwMC 7zjxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14751.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.017 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: locally refined map
File | emd_14751_additional_1.map | ||||||||||||
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Annotation | locally refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14751_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14751_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 80S-Selenosome
+Supramolecule #1: 80S-Selenosome
+Supramolecule #2: eEFSec and SECIS Binding Protein 2
+Supramolecule #3: Ser-tRNA-Sec
+Supramolecule #4: CrPV IRES
+Supramolecule #5: GPX4 SECIS element
+Supramolecule #6: 80S Ribosome
+Macromolecule #1: eEFSec
+Macromolecule #5: SECIS Binding Protein 2
+Macromolecule #9: 60S ribosomal protein uL2
+Macromolecule #10: 60S ribosomal protein L3
+Macromolecule #11: 60S ribosomal protein L4
+Macromolecule #12: Ribosomal_L18_c domain-containing protein
+Macromolecule #13: 60S ribosomal protein L6
+Macromolecule #14: 60S ribosomal Protein uL30
+Macromolecule #15: 60S ribosomal protein eL8
+Macromolecule #16: 60S ribosomal protein L9
+Macromolecule #17: 60S ribosomal protein L10
+Macromolecule #18: 60S ribosomal protein L11
+Macromolecule #19: 60S ribosomal protein eL13
+Macromolecule #20: 60S ribosomal protein L14
+Macromolecule #21: 60S ribosomal protein L15
+Macromolecule #22: 60S ribosomal protein uL13
+Macromolecule #23: 60S ribosomal protein uL22
+Macromolecule #24: 60S ribosomal Protein eL18
+Macromolecule #25: 60S ribosomal protein L19
+Macromolecule #26: 60S ribosomal protein eL20
+Macromolecule #27: 60S ribosomal protein eL21
+Macromolecule #28: 60S ribosomal protein eL22
+Macromolecule #29: 60S ribosomal protein L23
+Macromolecule #30: 60S ribosomal protein eL24
+Macromolecule #31: 60S ribosomal protein uL23
+Macromolecule #32: 60S ribosomal protein L26
+Macromolecule #33: 60S ribosomal protein L27
+Macromolecule #34: 60S ribosomal protein L27a
+Macromolecule #35: 60S ribosomal protein L29
+Macromolecule #36: 60S ribosomal protein eL30
+Macromolecule #37: 60S ribosomal protein eL31
+Macromolecule #38: 60S ribosomal protein eL32
+Macromolecule #39: 60S ribosomal protein eL33
+Macromolecule #40: 60S ribosomal protein L34
+Macromolecule #41: 60S ribosomal protein uL29
+Macromolecule #42: 60S ribosomal protein L36
+Macromolecule #43: 60S ribosomal protein L37
+Macromolecule #44: 60S ribosomal protein eL38
+Macromolecule #45: 60S ribosomal protein eL39
+Macromolecule #46: 60S ribosomal protein L40
+Macromolecule #47: 60S ribosomal protein eL42
+Macromolecule #48: 60S ribosomal protein eL43
+Macromolecule #49: 60S ribosomal protein eL28
+Macromolecule #50: 60S ribosomal protein P0
+Macromolecule #51: 60S ribosomal protein uL1
+Macromolecule #53: 40S ribosomal protein S27
+Macromolecule #54: 40S ribosomal protein S28
+Macromolecule #55: 40S ribosomal protein S27a
+Macromolecule #56: 40S ribosomal protein S30
+Macromolecule #57: Ribosomal protein eS26
+Macromolecule #58: RACK1
+Macromolecule #59: 40S ribosomal protein uS14
+Macromolecule #60: 40S ribosomal protein SA
+Macromolecule #61: 40S ribosomal protein S3a
+Macromolecule #62: 40S ribosomal protein uS5
+Macromolecule #63: 40S ribosomal protein S3
+Macromolecule #64: 40S ribosomal protein eS4
+Macromolecule #65: Ribosomal protein S5
+Macromolecule #66: 40S ribosomal protein S6
+Macromolecule #67: 40S ribosomal protein S7
+Macromolecule #68: 40S ribosomal protein S8
+Macromolecule #69: 40S ribosomal protein S9
+Macromolecule #70: 40S ribosomal protein eS10
+Macromolecule #71: 40S ribosomal protein S11
+Macromolecule #72: 40S ribosomal protein S12
+Macromolecule #73: 40S ribosomal protein uS15
+Macromolecule #74: 40S ribosomal protein uS11
+Macromolecule #75: 40S ribosomal protein uS19
+Macromolecule #76: 40S ribosomal protein uS9
+Macromolecule #77: 40S ribosomal protein eS17
+Macromolecule #78: 40S ribosomal protein S18
+Macromolecule #79: 40S Ribosomal protein eS19
+Macromolecule #80: 40S ribosomal protein uS10
+Macromolecule #81: 40S ribosomal protein eS21
+Macromolecule #82: 40S ribosomal protein S15a
+Macromolecule #83: 40S ribosomal protein S23
+Macromolecule #84: 40S ribosomal protein S24
+Macromolecule #85: 40S ribosomal protein S25
+Macromolecule #86: 60S ribosomal protein L41
+Macromolecule #2: human Ser-tRNA-Sec
+Macromolecule #3: CrPV IRES
+Macromolecule #4: GPX4 SECIS element
+Macromolecule #6: 28S rRNA
+Macromolecule #7: 5S rRNA
+Macromolecule #8: 5.8S rRNA
+Macromolecule #52: 18S rRNA
+Macromolecule #87: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #88: SERINE
+Macromolecule #89: MAGNESIUM ION
+Macromolecule #90: POTASSIUM ION
+Macromolecule #91: ZINC ION
+Macromolecule #92: SODIUM ION
+Macromolecule #93: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R3/3 / Material: COPPER/RHODIUM / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / 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 | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 13921 / Average electron dose: 30.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |