+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14752 | |||||||||
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Title | Rabbit 80S ribosome programmed with SECIS and SBP2 | |||||||||
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 / selenocysteine insertion sequence binding / 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 ...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 / selenocysteine insertion sequence binding / 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) / striatum development / negative regulation of RNA splicing / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / exit from mitosis / laminin receptor activity / optic nerve development / Ribosomal scanning and start codon recognition / Translation initiation complex formation / retinal ganglion cell axon guidance / mammalian oogenesis stage / organelle membrane / activation-induced cell death of T cells / Protein hydroxylation / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / 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 / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / protein-RNA complex assembly / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribonucleoprotein complex binding / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / translation regulator activity / laminin binding / cytosolic ribosome / rough endoplasmic reticulum / 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) / gastrulation / MDM2/MDM4 family protein binding / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / 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) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / mRNA 3'-UTR binding / small-subunit processome / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / spindle / Regulation of expression of SLITs and ROBOs / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / ribosomal small subunit biogenesis / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / glucose homeostasis / retina development in camera-type eye / regulation of translation / heparin binding / virus receptor activity / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / cytosolic small ribosomal subunit Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Oryctolagus cuniculus (rabbit) / Cricket paralysis virus / Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 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_14752.map.gz | 32.7 MB | EMDB map data format | |
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Header (meta data) | emd-14752-v30.xml emd-14752.xml | 122.3 KB 122.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14752_fsc.xml | 10.9 KB | Display | FSC data file |
Images | emd_14752.png | 99.4 KB | ||
Filedesc metadata | emd-14752.cif.gz | 23.3 KB | ||
Others | emd_14752_additional_1.map.gz emd_14752_half_map_1.map.gz emd_14752_half_map_2.map.gz | 69.2 MB 127.1 MB 127.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14752 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14752 | HTTPS FTP |
-Validation report
Summary document | emd_14752_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_14752_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_14752_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_14752_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14752 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14752 | HTTPS FTP |
-Related structure data
Related structure data | 7zjxMC 7zjwC 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_14752.map.gz / Format: CCP4 / Size: 137.1 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: 1.24 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_14752_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14752_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14752_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 80S-SBP2-SECIS
+Supramolecule #1: 80S-SBP2-SECIS
+Supramolecule #2: Selenocysteine insertion sequence-binding protein 2
+Supramolecule #3: 80S Ribosome
+Supramolecule #4: CrPV IRES
+Supramolecule #5: GPX4 SECIS element
+Macromolecule #1: Selenocysteine insertion sequence-binding protein 2
+Macromolecule #6: 60S ribosomal protein uL2
+Macromolecule #7: 60S ribosomal protein uL3
+Macromolecule #8: 60S ribosomal protein L4
+Macromolecule #9: Ribosomal_L18_c domain-containing protein
+Macromolecule #10: 60S ribosomal protein L6
+Macromolecule #11: 60S ribosomal Protein uL30
+Macromolecule #12: 60S ribosomal protein eL8
+Macromolecule #13: 60S ribosomal protein L9
+Macromolecule #14: Ribosomal protein L10
+Macromolecule #15: 60S ribosomal protein L11
+Macromolecule #16: 60S ribosomal protein eL13
+Macromolecule #17: 60S ribosomal protein L14
+Macromolecule #18: Ribosomal protein L15
+Macromolecule #19: 60S ribosomal protein uL13
+Macromolecule #20: 60S ribosomal protein uL22
+Macromolecule #21: 60S ribosomal Protein eL18
+Macromolecule #22: 60S ribosomal protein L19
+Macromolecule #23: 60S ribosomal protein eL20
+Macromolecule #24: 60S ribosomal protein L21
+Macromolecule #25: 60S ribosomal protein eL22
+Macromolecule #26: 60S ribosomal protein L23
+Macromolecule #27: Ribosomal protein L24
+Macromolecule #28: Ribosomal_L23eN domain-containing protein
+Macromolecule #29: Ribosomal protein L26
+Macromolecule #30: 60S ribosomal protein L27
+Macromolecule #31: 60S ribosomal protein L27a
+Macromolecule #32: 60S ribosomal protein L29
+Macromolecule #33: 60S ribosomal protein L30
+Macromolecule #34: 60S ribosomal protein L31
+Macromolecule #35: Ribosomal protein L32
+Macromolecule #36: 60S ribosomal protein L35a
+Macromolecule #37: 60S ribosomal protein L34
+Macromolecule #38: 60S ribosomal protein L35
+Macromolecule #39: 60S ribosomal protein L36
+Macromolecule #40: Ribosomal protein L37
+Macromolecule #41: 60S ribosomal protein L38
+Macromolecule #42: 60S ribosomal protein eL39
+Macromolecule #43: 60S ribosomal protein L40
+Macromolecule #44: 60S ribosomal protein eL42
+Macromolecule #45: 60S ribosomal protein eL43
+Macromolecule #46: 60S ribosomal protein eL28
+Macromolecule #47: Ribosomal protein
+Macromolecule #50: 40S ribosomal protein S27
+Macromolecule #51: 40S ribosomal protein S28
+Macromolecule #52: Ubiquitin carboxyl extension protein 80
+Macromolecule #53: 40S ribosomal protein S30
+Macromolecule #54: 40S ribosomal protein eS26
+Macromolecule #55: Guanine nucleotide-binding protein subunit beta-2-like 1
+Macromolecule #56: 40S ribosomal protein S29
+Macromolecule #57: 40S ribosomal protein SA
+Macromolecule #58: 40S ribosomal protein S3a
+Macromolecule #59: 40S ribosomal protein uS5
+Macromolecule #60: 40S ribosomal protein S3
+Macromolecule #61: 40S ribosomal protein S4
+Macromolecule #62: Ribosomal protein S5
+Macromolecule #63: 40S ribosomal protein S6
+Macromolecule #64: 40S ribosomal protein S7
+Macromolecule #65: 40S ribosomal protein S8
+Macromolecule #66: 40S ribosomal protein S9
+Macromolecule #67: S10_plectin domain-containing protein
+Macromolecule #68: 40S ribosomal protein S11
+Macromolecule #69: 40S ribosomal protein S12
+Macromolecule #70: 40S ribosomal protein S13
+Macromolecule #71: 40S ribosomal protein uS11
+Macromolecule #72: 40S ribosomal protein S15
+Macromolecule #73: 40S ribosomal protein uS9
+Macromolecule #74: 40S ribosomal protein S17
+Macromolecule #75: 40S ribosomal protein S18
+Macromolecule #76: 40S Ribosomal protein eS19
+Macromolecule #77: 40S ribosomal protein S20
+Macromolecule #78: 40S ribosomal protein eS21
+Macromolecule #79: 40S ribosomal protein S15a
+Macromolecule #80: 40S ribosomal protein S23
+Macromolecule #81: 40S ribosomal protein S24
+Macromolecule #82: 40S ribosomal protein S25
+Macromolecule #83: 60S ribosomal protein L41
+Macromolecule #2: CrPV IRES
+Macromolecule #3: 28S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #5: 5.8S rRNA
+Macromolecule #48: GPX4 SECIS element
+Macromolecule #49: 18S rRNA
+Macromolecule #84: ZINC ION
-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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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 6908 / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |