+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40344 | ||||||||||||
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Title | Terminating ribosome with SRI-41315 | ||||||||||||
Map data | unsharpened map | ||||||||||||
Sample |
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Keywords | termination / SRI-41315 / RIBOSOME | ||||||||||||
Function / homology | Function and homology information translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / ribosomal subunit / protein methylation / mammalian oogenesis stage / activation-induced cell death of T cells ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / ribosomal subunit / protein methylation / mammalian oogenesis stage / activation-induced cell death of T cells / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / regulation of G1 to G0 transition / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / 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 / G1 to G0 transition / T cell proliferation involved in immune response / Protein hydroxylation / erythrocyte development / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / TOR signaling / ribosomal small subunit export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / cellular response to actinomycin D / translational termination / 90S preribosome / rough endoplasmic reticulum / gastrulation / cytosolic ribosome / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / rescue of stalled ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / positive regulation of translation / positive regulation of apoptotic signaling pathway / small-subunit processome / placenta development / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / Regulation of expression of SLITs and ROBOs / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / spindle / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / positive regulation of canonical Wnt signaling pathway / rhythmic process / ribosome biogenesis / ribosome binding / glucose homeostasis / regulation of translation / T cell differentiation in thymus / cell body / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / mitochondrial inner membrane / tRNA binding / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of apoptotic process / positive regulation of protein phosphorylation / cell cycle / cell division / DNA repair / mRNA binding Similarity search - Function | ||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||
Authors | Yip MCJ / Coelho JPL / Oltion K / Tauton J / Shao S | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: Structure and consequences of eRF1 glued to the ribosomal decoding center Authors: Coelho JPL / Yip MCJ / Oltion K / Taunton J / Shao S | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40344.map.gz | 335.9 MB | EMDB map data format | |
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Header (meta data) | emd-40344-v30.xml emd-40344.xml | 110.4 KB 110.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40344_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_40344.png | 150.7 KB | ||
Filedesc metadata | emd-40344.cif.gz | 22.2 KB | ||
Others | emd_40344_additional_1.map.gz emd_40344_additional_2.map.gz emd_40344_half_map_1.map.gz emd_40344_half_map_2.map.gz | 101.1 MB 356.6 MB 337.3 MB 337.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40344 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40344 | HTTPS FTP |
-Related structure data
Related structure data | 8scbMC 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_40344.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | unsharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: sharpened map
File | emd_40344_additional_1.map | ||||||||||||
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Annotation | sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: deepEMhancer processed map
File | emd_40344_additional_2.map | ||||||||||||
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Annotation | deepEMhancer processed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half2
File | emd_40344_half_map_1.map | ||||||||||||
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Annotation | half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half1
File | emd_40344_half_map_2.map | ||||||||||||
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Annotation | half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : terminating rabbit ribosome
+Supramolecule #1: terminating rabbit ribosome
+Macromolecule #1: Ribosomal protein L8
+Macromolecule #2: Ribosomal protein L3
+Macromolecule #3: 60S ribosomal protein L4
+Macromolecule #4: Ribosomal_L18_c domain-containing protein
+Macromolecule #5: 60S ribosomal protein L6
+Macromolecule #6: 60S ribosomal protein L7
+Macromolecule #7: 60S ribosomal protein L7a
+Macromolecule #8: 60S ribosomal protein L9
+Macromolecule #9: 60S ribosomal protein L10
+Macromolecule #10: 60S ribosomal protein L11
+Macromolecule #11: eL13
+Macromolecule #12: 60S ribosomal protein L14
+Macromolecule #13: Ribosomal protein L15
+Macromolecule #14: uL13
+Macromolecule #15: uL22
+Macromolecule #16: Ribosomal protein L18
+Macromolecule #17: Ribosomal protein L19
+Macromolecule #18: eL20
+Macromolecule #19: eL21
+Macromolecule #20: eL22
+Macromolecule #21: Ribosomal protein L23
+Macromolecule #22: 60S ribosomal protein L24
+Macromolecule #23: eL23
+Macromolecule #24: uL24
+Macromolecule #25: 60S ribosomal protein L27
+Macromolecule #26: 60S ribosomal protein L27a
+Macromolecule #27: 60S ribosomal protein L29
+Macromolecule #28: eL30
+Macromolecule #29: eL31
+Macromolecule #30: eL32
+Macromolecule #31: eL33
+Macromolecule #32: 60S ribosomal protein L34
+Macromolecule #33: eL35
+Macromolecule #34: 60S ribosomal protein L36
+Macromolecule #35: Ribosomal protein L37
+Macromolecule #36: 60S ribosomal protein L38
+Macromolecule #37: eL39
+Macromolecule #38: Ubiquitin A-52 residue ribosomal protein fusion product 1
+Macromolecule #39: eL41
+Macromolecule #40: eL42
+Macromolecule #41: eL43
+Macromolecule #42: eL28
+Macromolecule #43: 60S acidic ribosomal protein P0
+Macromolecule #44: 60S ribosomal protein L12
+Macromolecule #45: NC
+Macromolecule #52: uS2 (SA)
+Macromolecule #53: eS1
+Macromolecule #54: uS5
+Macromolecule #55: Ribosomal protein S3
+Macromolecule #56: eS4 (S4 X isoform)
+Macromolecule #57: uS7
+Macromolecule #58: eS6
+Macromolecule #59: eS7
+Macromolecule #60: eS8
+Macromolecule #61: uS4
+Macromolecule #62: S10_plectin domain-containing protein
+Macromolecule #63: uS17
+Macromolecule #64: eS12
+Macromolecule #65: uS15
+Macromolecule #66: uS11
+Macromolecule #67: uS19
+Macromolecule #68: uS9
+Macromolecule #69: eS17
+Macromolecule #70: uS13
+Macromolecule #71: eS19
+Macromolecule #72: uS10
+Macromolecule #73: eS21
+Macromolecule #74: uS8
+Macromolecule #75: uS12
+Macromolecule #76: 40S ribosomal protein S24
+Macromolecule #77: eS25
+Macromolecule #78: 40S ribosomal protein S26
+Macromolecule #79: eS27
+Macromolecule #80: eS28
+Macromolecule #81: uS14
+Macromolecule #82: eS30
+Macromolecule #83: eS31
+Macromolecule #84: Receptor for Activated C Kinase 1 (RACK1)
+Macromolecule #86: Eukaryotic peptide chain release factor subunit 1
+Macromolecule #87: ATP binding cassette subfamily E member 1
+Macromolecule #46: P_tRNA
+Macromolecule #47: E_tRNA
+Macromolecule #48: 28S_rRNA
+Macromolecule #49: 5S_rRNA
+Macromolecule #50: 5.8S_rRNA
+Macromolecule #51: 18S_rRNA
+Macromolecule #85: mRNA
+Macromolecule #88: MAGNESIUM ION
+Macromolecule #89: ZINC ION
+Macromolecule #90: (2S,4aS)-2-cyclobutyl-10-methyl-3-phenyl-2,10-dihydropyrimido[4,5...
+Macromolecule #91: IRON/SULFUR CLUSTER
+Macromolecule #92: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |