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Yorodumi- EMDB-4130: Structure of the mammalian ribosomal elongation complex with amin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4130 | ||||||||||||
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Title | Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin B | ||||||||||||
Map data | Postprocessed, sharpened map. | ||||||||||||
Sample |
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Function / homology | Function and homology information : / guanyl nucleotide binding / positive regulation by host of viral genome replication / 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 ...: / guanyl nucleotide binding / positive regulation by host of viral genome replication / 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 / cortical actin cytoskeleton / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / 90S preribosome / T cell proliferation involved in immune response / translation elongation factor activity / erythrocyte development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal small subunit export from nucleus / translation regulator activity / cytosolic ribosome / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / cellular response to epidermal growth factor stimulus / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / small-subunit processome / positive regulation of translation / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / spindle / ruffle membrane / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosomal small subunit biogenesis / positive regulation of canonical Wnt signaling pathway / rhythmic process / small ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / glucose homeostasis / retina development in camera-type eye / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / cytosolic small ribosomal subunit / perikaryon / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / cytoplasmic translation / killing of cells of another organism / tRNA binding / mitochondrial inner membrane / molecular adaptor activity / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell division / DNA repair / GTPase activity / mRNA binding / centrosome Similarity search - Function | ||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.31 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. #1: Journal: To Be Published 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4130.map.gz | 23.5 MB | EMDB map data format | |
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Header (meta data) | emd-4130-v30.xml emd-4130.xml | 101 KB 101 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4130_fsc.xml | 16.4 KB | Display | FSC data file |
Images | emd_4130.png | 186.9 KB | ||
Others | emd_4130_half_map_1.map.gz emd_4130_half_map_2.map.gz | 315.6 MB 315.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4130 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4130 | HTTPS FTP |
-Validation report
Summary document | emd_4130_validation.pdf.gz | 415.5 KB | Display | EMDB validaton report |
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Full document | emd_4130_full_validation.pdf.gz | 414.5 KB | Display | |
Data in XML | emd_4130_validation.xml.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4130 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4130 | HTTPS FTP |
-Related structure data
Related structure data | 5lzsMC 4129C 4131C 4132C 4133C 4134C 4135C 4136C 4137C 5lztC 5lzuC 5lzvC 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_4130.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed, sharpened map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 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_4130_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_4130_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 stalled with...
+Supramolecule #1: Affinity-purified 80S ribosome-nascent chain complex stalled with...
+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: uL14
+Macromolecule #22: uL24
+Macromolecule #23: uL23
+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: Ribosomal protein L37
+Macromolecule #36: eL38
+Macromolecule #37: eL39
+Macromolecule #38: eL40
+Macromolecule #39: 60s ribosomal protein l41
+Macromolecule #40: eL42
+Macromolecule #41: eL43
+Macromolecule #42: eL28
+Macromolecule #43: uL10
+Macromolecule #44: uL11
+Macromolecule #51: uS2
+Macromolecule #52: 40S ribosomal protein S3a
+Macromolecule #53: uS5
+Macromolecule #54: uS4
+Macromolecule #55: 40S ribosomal protein S4
+Macromolecule #56: Uncharacterized protein
+Macromolecule #57: 40S ribosomal protein S6
+Macromolecule #58: uS7
+Macromolecule #59: 40S ribosomal protein S8
+Macromolecule #60: Ribosomal protein S9 (Predicted)
+Macromolecule #61: eS10
+Macromolecule #62: uS17
+Macromolecule #63: 40S ribosomal protein S12
+Macromolecule #64: uS15
+Macromolecule #65: uS11
+Macromolecule #66: uS19
+Macromolecule #67: uS9
+Macromolecule #68: eS17
+Macromolecule #69: uS13
+Macromolecule #70: eS19
+Macromolecule #71: uS10
+Macromolecule #72: eS21
+Macromolecule #73: uS8
+Macromolecule #74: uS12
+Macromolecule #75: eS24
+Macromolecule #76: eS25
+Macromolecule #77: eS26
+Macromolecule #78: 40S ribosomal protein S27
+Macromolecule #79: eS28
+Macromolecule #80: uS14
+Macromolecule #81: eS30
+Macromolecule #82: eS31
+Macromolecule #83: RACK1
+Macromolecule #85: Elongation factor 1-alpha 1
+Macromolecule #45: tRNA
+Macromolecule #46: E-site tRNA
+Macromolecule #47: 28S ribosomal RNA
+Macromolecule #48: 5S ribosomal RNA
+Macromolecule #49: 5.8S ribosomal RNA
+Macromolecule #50: 18S ribosomal RNA
+Macromolecule #84: mRNA
+Macromolecule #86: MAGNESIUM ION
+Macromolecule #87: ZINC ION
+Macromolecule #88: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #89: (2~{S})-~{N}-[(2~{R})-1-[[(3~{S},6~{S},8~{S},12~{S},13~{R},16~{S}...
-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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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number real images: 1627 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 134615 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 69000 |
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
Details | Restraints for didemnin B were derived from Phenix.elbow and Mogul. |
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Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 64.8 / Target criteria: FSCaverage |
Output model | PDB-5lzs: |