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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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Function / homology | Function and homology information translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Protein hydroxylation / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / ribosome binding / 5S rRNA binding / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleolus / ATP hydrolysis activity / RNA binding / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | ||||||||||||
Authors | Shao S / Murray J / Brown A / Taunton J / Ramakrishnan V / Hegde RS | ||||||||||||
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 | 101.5 KB 101.5 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 | ||
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 |
-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: 5.0 nm / 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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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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 59000 |
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 / Number real images: 5706 / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2 |
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: |