[English] 日本語

- EMDB-38660: State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 t... -
+
Open data
-
Basic information
Entry | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation | ||||||||||||
![]() | A_P_rotated_80S ribosome | ||||||||||||
![]() |
| ||||||||||||
![]() | 80S / compact eEF2 / elongation cycle / rotated / TRANSLATION | ||||||||||||
Function / homology | ![]() Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / nonfunctional rRNA decay / response to cycloheximide / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of translational frameshifting / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / positive regulation of protein kinase activity / Ub-specific processing proteases / translation elongation factor activity / ribosomal subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational termination / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / Neutrophil degranulation / cellular response to amino acid starvation / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein kinase C binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / small-subunit processome / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / protein-folding chaperone binding / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / G protein-coupled receptor signaling pathway / translation / ribonucleoprotein complex / negative regulation of gene expression / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
![]() | Cheng J / Wu CL / Li JX / Zhang XZ | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Snapshots of ribosome dynamics near atomic resolution in situ: a full insight into eukaryotic elongation cycle Authors: Cheng J / Wu CL / Li JX / Yang Q / Zhao MJ / Zhang XZ | ||||||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 230 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 98.6 KB 98.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.8 KB | Display | ![]() |
Images | ![]() | 119.9 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 18.3 KB | ||
Others | ![]() ![]() | 226.4 MB 226.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xu8MC ![]() 8yldC ![]() 8ylrC ![]() 8z70C ![]() 8z71C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | A_P_rotated_80S ribosome | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map
File | emd_38660_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half_map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map
File | emd_38660_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half_map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
+Entire : Yeast 80S ribosome with compact eEF2 and tRNAs
+Supramolecule #1: Yeast 80S ribosome with compact eEF2 and tRNAs
+Macromolecule #1: 18S rRNA
+Macromolecule #2: 25S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #46: tRNA
+Macromolecule #5: Large ribosomal subunit protein uL2A
+Macromolecule #6: Large ribosomal subunit protein uL3
+Macromolecule #7: Large ribosomal subunit protein uL4A
+Macromolecule #8: Large ribosomal subunit protein uL18
+Macromolecule #9: Large ribosomal subunit protein eL6B
+Macromolecule #10: Large ribosomal subunit protein uL30A
+Macromolecule #11: Large ribosomal subunit protein eL8A
+Macromolecule #12: Large ribosomal subunit protein uL6A
+Macromolecule #13: Large ribosomal subunit protein uL16
+Macromolecule #14: Large ribosomal subunit protein uL5B
+Macromolecule #15: Large ribosomal subunit protein eL13A
+Macromolecule #16: Large ribosomal subunit protein eL14A
+Macromolecule #17: Large ribosomal subunit protein eL15A
+Macromolecule #18: Large ribosomal subunit protein uL13A
+Macromolecule #19: Large ribosomal subunit protein uL22A
+Macromolecule #20: Large ribosomal subunit protein eL18A
+Macromolecule #21: Large ribosomal subunit protein eL19A
+Macromolecule #22: Large ribosomal subunit protein eL20A
+Macromolecule #23: Large ribosomal subunit protein eL21A
+Macromolecule #24: Large ribosomal subunit protein eL22A
+Macromolecule #25: Large ribosomal subunit protein uL14A
+Macromolecule #26: Large ribosomal subunit protein eL24A
+Macromolecule #27: Large ribosomal subunit protein uL23
+Macromolecule #28: Large ribosomal subunit protein uL24A
+Macromolecule #29: Large ribosomal subunit protein eL27A
+Macromolecule #30: Large ribosomal subunit protein uL15
+Macromolecule #31: Large ribosomal subunit protein eL29
+Macromolecule #32: Large ribosomal subunit protein eL30
+Macromolecule #33: Large ribosomal subunit protein eL31A
+Macromolecule #34: Large ribosomal subunit protein eL32
+Macromolecule #35: Large ribosomal subunit protein eL33A
+Macromolecule #36: Large ribosomal subunit protein eL34A
+Macromolecule #37: Large ribosomal subunit protein uL29A
+Macromolecule #38: Large ribosomal subunit protein eL36A
+Macromolecule #39: Large ribosomal subunit protein eL37A
+Macromolecule #40: Large ribosomal subunit protein eL38
+Macromolecule #41: Large ribosomal subunit protein eL39
+Macromolecule #42: Large ribosomal subunit protein eL40A
+Macromolecule #43: Large ribosomal subunit protein eL41A
+Macromolecule #44: Large ribosomal subunit protein eL42A
+Macromolecule #45: Large ribosomal subunit protein eL43A
+Macromolecule #47: Elongation factor 2
+Macromolecule #48: Small ribosomal subunit protein eS12
+Macromolecule #49: Small ribosomal subunit protein uS11B
+Macromolecule #50: Small ribosomal subunit protein eS26A
+Macromolecule #51: Small ribosomal subunit protein eS10A
+Macromolecule #52: Small ribosomal subunit protein uS19
+Macromolecule #53: Small ribosomal subunit protein uS3
+Macromolecule #54: Small ribosomal subunit protein eS19A
+Macromolecule #55: Small ribosomal subunit protein uS10
+Macromolecule #56: Small ribosomal subunit protein eS28A
+Macromolecule #57: Small ribosomal subunit protein uS14A
+Macromolecule #58: Small ribosomal subunit protein uS7
+Macromolecule #59: Small ribosomal subunit protein uS9A
+Macromolecule #60: Small ribosomal subunit protein uS13A
+Macromolecule #61: Small ribosomal subunit protein RACK1
+Macromolecule #62: Small ribosomal subunit protein eS31
+Macromolecule #63: Small ribosomal subunit protein eS17A
+Macromolecule #64: Small ribosomal subunit protein uS2A
+Macromolecule #65: Small ribosomal subunit protein eS1A
+Macromolecule #66: Small ribosomal subunit protein uS5
+Macromolecule #67: Small ribosomal subunit protein eS4A
+Macromolecule #68: Small ribosomal subunit protein eS6A
+Macromolecule #69: Small ribosomal subunit protein eS7A
+Macromolecule #70: Small ribosomal subunit protein eS8A
+Macromolecule #71: Small ribosomal subunit protein uS4A
+Macromolecule #72: Small ribosomal subunit protein uS17A
+Macromolecule #73: Small ribosomal subunit protein uS15
+Macromolecule #74: Small ribosomal subunit protein eS21A
+Macromolecule #75: Small ribosomal subunit protein uS8A
+Macromolecule #76: Small ribosomal subunit protein uS12A
+Macromolecule #77: Small ribosomal subunit protein eS24A
+Macromolecule #78: Small ribosomal subunit protein eS27A
+Macromolecule #79: Small ribosomal subunit protein eS30A
+Macromolecule #80: Small ribosomal subunit protein eS25A
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | cell |
-
Sample preparation
Buffer | pH: 4.5 / Details: YPD |
---|---|
Grid | Material: COPPER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |