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Yorodumi- EMDB-4136: Structure of the mammalian rescue complex with Pelota and Hbs1l a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4136 | ||||||||||||
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Title | Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a polyadenylated mRNA. | ||||||||||||
Map data | Postprocessed, sharpened map. | ||||||||||||
Sample |
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Function / homology | Function and homology information stalled ribosome sensor activity / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / mRNA decay by 3' to 5' exoribonuclease / mesenchymal to epithelial transition / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / endoderm development ...stalled ribosome sensor activity / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / mRNA decay by 3' to 5' exoribonuclease / mesenchymal to epithelial transition / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / endoderm development / positive regulation of BMP signaling pathway / inner cell mass cell proliferation / stem cell population maintenance / chromosome organization / translation elongation factor activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding / regulation of translation / 5S rRNA binding / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / cell cycle / ribonucleoprotein complex / translation / cell division / GTPase activity / GTP binding / nucleolus / signal transduction / RNA binding / extracellular exosome / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.99 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_4136.map.gz | 13.5 MB | EMDB map data format | |
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Header (meta data) | emd-4136-v30.xml emd-4136.xml | 100.3 KB 100.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4136_fsc.xml | 14.6 KB | Display | FSC data file |
Images | emd_4136.png | 189 KB | ||
Others | emd_4136_half_map_1.map.gz emd_4136_half_map_2.map.gz | 247.8 MB 248.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4136 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4136 | HTTPS FTP |
-Related structure data
Related structure data | 5lzyMC 4129C 4130C 4131C 4132C 4133C 4134C 4135C 4137C 5lzsC 5lztC 5lzuC 5lzvC 5lzwC 5lzxC 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_4136.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_4136_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_4136_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 reconstitute...
+Supramolecule #1: Affinity-purified 80S ribosome-nascent chain complex reconstitute...
+Macromolecule #1: uL2
+Macromolecule #2: uL3
+Macromolecule #3: uL4
+Macromolecule #4: 60S ribosomal protein L5
+Macromolecule #5: 60S ribosomal protein L6
+Macromolecule #6: uL30
+Macromolecule #7: eL8
+Macromolecule #8: uL6
+Macromolecule #9: Ribosomal protein L10 (Predicted)
+Macromolecule #10: uL5
+Macromolecule #11: eL13
+Macromolecule #12: eL14
+Macromolecule #13: Ribosomal protein L15
+Macromolecule #14: uL13
+Macromolecule #15: uL22
+Macromolecule #16: eL18
+Macromolecule #17: eL19
+Macromolecule #18: eL20
+Macromolecule #19: eL21
+Macromolecule #20: eL22
+Macromolecule #21: eL14
+Macromolecule #22: eL24
+Macromolecule #23: eL23
+Macromolecule #24: uL24
+Macromolecule #25: 60S ribosomal protein L27
+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: 60S ribosomal protein L36
+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 #50: uS2
+Macromolecule #51: 40S ribosomal protein S3a
+Macromolecule #52: uS5
+Macromolecule #53: uS3
+Macromolecule #54: eS4
+Macromolecule #55: uS7
+Macromolecule #56: 40S ribosomal protein S6
+Macromolecule #57: eS7
+Macromolecule #58: eS8
+Macromolecule #59: Ribosomal protein S9 (Predicted)
+Macromolecule #60: eS10
+Macromolecule #61: uS17
+Macromolecule #62: 40S ribosomal protein S12
+Macromolecule #63: uS15
+Macromolecule #64: uS11
+Macromolecule #65: uS19
+Macromolecule #66: uS9
+Macromolecule #67: eS17
+Macromolecule #68: uS13
+Macromolecule #69: eS19
+Macromolecule #70: uS10
+Macromolecule #71: eS21
+Macromolecule #72: uS8
+Macromolecule #73: uS12
+Macromolecule #74: eS24
+Macromolecule #75: eS25
+Macromolecule #76: eS26
+Macromolecule #77: 40S ribosomal protein S27
+Macromolecule #78: eS28
+Macromolecule #79: uS14
+Macromolecule #80: eS30
+Macromolecule #81: eS31
+Macromolecule #82: RACK1
+Macromolecule #84: Protein pelota homolog
+Macromolecule #85: HBS1-like protein
+Macromolecule #45: tRNA
+Macromolecule #46: 28S ribosomal RNA
+Macromolecule #47: 5S ribosomal RNA
+Macromolecule #48: 5.8S ribosomal RNA
+Macromolecule #49: 18S ribosomal RNA
+Macromolecule #83: mRNA (polyadenylated)
+Macromolecule #86: MAGNESIUM ION
+Macromolecule #87: ZINC ION
+Macromolecule #88: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
-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: 1112 / 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: 63.6 / Target criteria: FSCaverage |
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Output model | PDB-5lzy: |