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Yorodumi- EMDB-4133: Structure of the mammalian ribosomal termination complex with acc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4133 | ||||||||||||
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Title | Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1. | ||||||||||||
Map data | Postprocessed, sharpened map. | ||||||||||||
Sample |
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Keywords | Translation / Elongation / 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 / protein methylation / sequence-specific mRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / aminoacyl-tRNA hydrolase activity ...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 / protein methylation / sequence-specific mRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / aminoacyl-tRNA hydrolase activity / regulation of G1 to G0 transition / exit from mitosis / 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 / optic nerve development / mammalian oogenesis stage / retinal ganglion cell axon guidance / G1 to G0 transition / activation-induced cell death of T cells / Protein hydroxylation / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / ribosomal small subunit binding / TOR signaling / T cell proliferation involved in immune response / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / ribosomal subunit export from nucleus / translational termination / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translational initiation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / protein tag activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome binding / retina development in camera-type eye / glucose homeostasis / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / perikaryon / cytosolic small ribosomal subunit / defense response to Gram-negative bacterium / killing of cells of another organism / cytosolic large ribosomal subunit / mitochondrial inner membrane / tRNA binding / cytoplasmic translation / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome Similarity search - Function | ||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | ||||||||||||
Authors | Shao S / Murray J | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Cell / Year: 2016 Title: Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes. Authors: Sichen Shao / Jason Murray / Alan Brown / Jack Taunton / V Ramakrishnan / Ramanujan S Hegde / Abstract: In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the ...In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the mammalian ribosome engaged with decoding factor⋅GTPase complexes representing intermediates of translation elongation (aminoacyl-tRNA⋅eEF1A), termination (eRF1⋅eRF3), and ribosome rescue (Pelota⋅Hbs1l). Comparative analyses reveal that each decoding factor exploits the plasticity of the ribosomal decoding center to differentially remodel ribosomal proteins and rRNA. This leads to varying degrees of large-scale ribosome movements and implies distinct mechanisms for communicating information from the decoding center to each GTPase. Additional structural snapshots of the translation termination pathway reveal the conformational changes that choreograph the accommodation of decoding factors into the peptidyl transferase center. Our results provide a structural framework for how different states of the mammalian ribosome are selectively recognized by the appropriate decoding factor⋅GTPase complex to ensure translational fidelity. | ||||||||||||
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_4133.map.gz | 14.1 MB | EMDB map data format | |
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Header (meta data) | emd-4133-v30.xml emd-4133.xml | 108 KB 108 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4133_fsc.xml | 14.6 KB | Display | FSC data file |
Images | emd_4133.png | 183 KB | ||
Filedesc metadata | emd-4133.cif.gz | 21.4 KB | ||
Others | emd_4133_half_map_1.map.gz emd_4133_half_map_2.map.gz | 251.4 MB 251.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4133 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4133 | HTTPS FTP |
-Validation report
Summary document | emd_4133_validation.pdf.gz | 384 KB | Display | EMDB validaton report |
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Full document | emd_4133_full_validation.pdf.gz | 383.1 KB | Display | |
Data in XML | emd_4133_validation.xml.gz | 20.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4133 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4133 | HTTPS FTP |
-Related structure data
Related structure data | 5lzvMC 4129C 4130C 4131C 4132C 4134C 4135C 4136C 4137C 5lzsC 5lztC 5lzuC 5lzwC 5lzxC 5lzyC 5lzzC 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_4133.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed, sharpened 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
-Half map: Half map 1.
File | emd_4133_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_4133_half_map_2.map | ||||||||||||
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Annotation | Half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Affinity-purified 80S ribosome-nascent chain complex with eRF1(AA...
+Supramolecule #1: Affinity-purified 80S ribosome-nascent chain complex with eRF1(AA...
+Macromolecule #1: uL2
+Macromolecule #2: uL3
+Macromolecule #3: uL4
+Macromolecule #4: uL18
+Macromolecule #5: eL6
+Macromolecule #6: uL30
+Macromolecule #7: eL8
+Macromolecule #8: uL6
+Macromolecule #9: uL16
+Macromolecule #10: uL5
+Macromolecule #11: eL13
+Macromolecule #12: eL14
+Macromolecule #13: eL15
+Macromolecule #14: uL13
+Macromolecule #15: uL22
+Macromolecule #16: eL18
+Macromolecule #17: eL19
+Macromolecule #18: eL20
+Macromolecule #19: eL21
+Macromolecule #20: eL22
+Macromolecule #21: uL14
+Macromolecule #22: eL24
+Macromolecule #23: uL23
+Macromolecule #24: uL24
+Macromolecule #25: eL27
+Macromolecule #26: uL15
+Macromolecule #27: eL29
+Macromolecule #28: eL30
+Macromolecule #29: eL31
+Macromolecule #30: eL32
+Macromolecule #31: eL33
+Macromolecule #32: eL34
+Macromolecule #33: uL29
+Macromolecule #34: eL36
+Macromolecule #35: eL37
+Macromolecule #36: eL38
+Macromolecule #37: eL39
+Macromolecule #38: eL40
+Macromolecule #39: eL41
+Macromolecule #40: eL42
+Macromolecule #41: eL43
+Macromolecule #42: eL28
+Macromolecule #43: uL10
+Macromolecule #44: uL11
+Macromolecule #45: Nascent chain
+Macromolecule #52: uS2
+Macromolecule #53: eS1
+Macromolecule #54: uS5
+Macromolecule #55: uS3
+Macromolecule #56: eS4
+Macromolecule #57: uS7
+Macromolecule #58: eS6
+Macromolecule #59: eS7
+Macromolecule #60: eS8
+Macromolecule #61: uS4
+Macromolecule #62: eS10
+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: eS24
+Macromolecule #77: eS25
+Macromolecule #78: eS26
+Macromolecule #79: eS27
+Macromolecule #80: eS28
+Macromolecule #81: uS14
+Macromolecule #82: eS30
+Macromolecule #83: eS31
+Macromolecule #84: RACK1
+Macromolecule #86: eRF1(AAQ)
+Macromolecule #87: ABCE1
+Macromolecule #46: P-site tRNA
+Macromolecule #47: E-site tRNA
+Macromolecule #48: 28S ribosomal RNA
+Macromolecule #49: 5S ribosomal RNA
+Macromolecule #50: 5.8S ribosomal RNA
+Macromolecule #51: 18S ribosomal RNA
+Macromolecule #85: mRNA (UGA stop codon)
+Macromolecule #88: MAGNESIUM ION
+Macromolecule #89: ZINC ION
+Macromolecule #90: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
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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 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III Details: 3 ul aliquots were applied to the grid and incubated for 30 s, before blotting for 3s to remove excess solution.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number real images: 5706 / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 66.4 / Target criteria: FSCaverage |
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Output model | PDB-5lzv: |