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- EMDB-4131: Structure of the mammalian ribosomal termination complex with eRF... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4131 | ||||||||||||
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Title | Structure of the mammalian ribosomal termination complex with eRF1 and eRF3. | ||||||||||||
![]() | Postprocess, sharpened map. | ||||||||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Shao S / Murray J / Brown A / Taunton J / Ramakrishnan V / Hegde RS | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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. #1: ![]() Title: Decoding mammalian ribosome-mRNA states by translational GTPase complexes Authors: Shao S / Murray J / Brown A / Taunton J / Ramakrishnan V / Hegde RS | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 13 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 102.2 KB 102.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.6 KB | Display | ![]() |
Images | ![]() | 185.8 KB | ||
Others | ![]() ![]() | 245.2 MB 245.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lztMC ![]() 4129C ![]() 4130C ![]() 4132C ![]() 4133C ![]() 4134C ![]() 4135C ![]() 4136C ![]() 4137C ![]() 5lzsC ![]() 5lzuC ![]() 5lzvC ![]() 5lzwC ![]() 5lzxC ![]() 5lzyC ![]() 5lzzC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocess, 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_4131_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_4131_half_map_2.map | ||||||||||||
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Annotation | Half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
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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: 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
+Macromolecule #87: eRF3a
+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: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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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.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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: 2611 / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 63.3 / Target criteria: FSCaverage |
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Output model | ![]() PDB-5lzt: |