[English] 日本語
Yorodumi- EMDB-12081: Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs (PRE-1) -
+
Open data
-
Basic information
| Entry | Database: EMDB / ID: EMD-12081 | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs (PRE-1) | |||||||||||||||
Map data | full 80S Map Post-Process | |||||||||||||||
Sample |
| |||||||||||||||
Keywords | eukaryotic Elongation Factor 3 / eEF3 / YEF3 / Translation / Elongation / ABCF | |||||||||||||||
| Function / homology | Function and homology informationcytoplasmic translational elongation / cytoplasmic translational termination / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling ...cytoplasmic translational elongation / cytoplasmic translational termination / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of translational frameshifting / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / positive regulation of protein kinase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / 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 / Ub-specific processing proteases / translation elongation factor activity / regulation of translational fidelity / protein-RNA complex assembly / translational termination / ribosomal subunit export from nucleus / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / 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) / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / cytosolic ribosome / rescue of stalled ribosome / protein kinase C binding / cellular response to amino acid starvation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
| Biological species | ![]() ![]() ![]() | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Ranjan N / Pochopien AA / Wu CC / Beckert B / Blanchet S / Green R / Rodnina MV / Wilson DN | |||||||||||||||
| Funding support | Germany, 4 items
| |||||||||||||||
Citation | Journal: To Be PublishedTitle: eEF3 promotes late stages of tRNA translocation including E-tRNA release from the ribosome Authors: Ranjan N / Pochopien AA / Wu CC / Beckert B / Blanchet S / Green R / Rodnina MV / Wilson DN | |||||||||||||||
| History |
|
-
Structure visualization
| Movie |
Movie viewer |
|---|---|
| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
-
Downloads & links
-EMDB archive
| Map data | emd_12081.map.gz | 23.4 MB | EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) | emd-12081-v30.xml emd-12081.xml | 132.2 KB 132.2 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_12081_fsc.xml | 14.9 KB | Display | FSC data file |
| Images | emd_12081.png | 93.1 KB | ||
| Filedesc metadata | emd-12081.cif.gz | 19.9 KB | ||
| Others | emd_12081_additional_1.map.gz emd_12081_additional_10.map.gz emd_12081_additional_2.map.gz emd_12081_additional_3.map.gz emd_12081_additional_4.map.gz emd_12081_additional_5.map.gz emd_12081_additional_6.map.gz emd_12081_additional_7.map.gz emd_12081_additional_8.map.gz emd_12081_additional_9.map.gz emd_12081_half_map_1.map.gz emd_12081_half_map_2.map.gz | 264.8 MB 264.4 MB 17.1 MB 265 MB 264.8 MB 264.7 MB 224.8 MB 7.7 MB 4.7 MB 264.4 MB 225.3 MB 226 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12081 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12081 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7b7dMC M: atomic model generated by this map C: citing same article ( |
|---|---|
| Similar structure data |
-
Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
|---|---|
| Related items in Molecule of the Month |
-
Map
| File | Download / File: emd_12081.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | full 80S Map Post-Process | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
CCP4 map header:
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Supplemental data
+Additional map: full Map Post-Process lowpass filtered to 5 Angstrom
+Additional map: Multibody Small subunit Head region Map Post-Process lowpass...
+Additional map: Multibody Large subunit Post-process
+Additional map: full Map Post-Process lowpass filtered to 4 Angstrom
+Additional map: Multibody Large subunit Map Post-Process lowpass filtered to...
+Additional map: Multibody Large subunit Map Post-Process lowpass filtered to...
+Additional map: Relion final refinement round
+Additional map: Multibody Small subunit body region Map Post-Process
+Additional map: Multibody Small subunit Head region Map Post-Process
+Additional map: Multibody Small subunit Head region Map Post-Process lowpass...
+Half map: Half map
+Half map: Half map
-
Sample components
+Entire : Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs
+Supramolecule #1: Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs
+Macromolecule #1: 18S rRNA
+Macromolecule #2: mRNA
+Macromolecule #36: 25S rRNA
+Macromolecule #37: 5S rRNA
+Macromolecule #38: 5.8S rRNA
+Macromolecule #80: tRNA
+Macromolecule #3: 40S ribosomal protein S0-A
+Macromolecule #4: 40S ribosomal protein S1-A
+Macromolecule #5: 40S ribosomal protein S15
+Macromolecule #6: 40S ribosomal protein S2
+Macromolecule #7: 40S ribosomal protein S3
+Macromolecule #8: 40S ribosomal protein S4-A
+Macromolecule #9: 40S ribosomal protein S5
+Macromolecule #10: 40S ribosomal protein S6-A
+Macromolecule #11: 40S ribosomal protein S7-A
+Macromolecule #12: 40S ribosomal protein S8-A
+Macromolecule #13: 40S ribosomal protein S9-A
+Macromolecule #14: 40S ribosomal protein S10-A
+Macromolecule #15: 40S ribosomal protein S11-A
+Macromolecule #16: 40S ribosomal protein S12
+Macromolecule #17: 40S ribosomal protein S13
+Macromolecule #18: 40S ribosomal protein S14-B
+Macromolecule #19: 40S ribosomal protein S16-A
+Macromolecule #20: 40S ribosomal protein S17-B
+Macromolecule #21: 40S ribosomal protein S18-A
+Macromolecule #22: 40S ribosomal protein S19-A
+Macromolecule #23: 40S ribosomal protein S20
+Macromolecule #24: 40S ribosomal protein S21-A
+Macromolecule #25: 40S ribosomal protein S22-A
+Macromolecule #26: 40S ribosomal protein S23-A
+Macromolecule #27: 40S ribosomal protein S24-A
+Macromolecule #28: 40S ribosomal protein S25-A
+Macromolecule #29: 40S ribosomal protein S26-B
+Macromolecule #30: 40S ribosomal protein S27-A
+Macromolecule #31: 40S ribosomal protein S29-A
+Macromolecule #32: 40S ribosomal protein S30-A
+Macromolecule #33: Ubiquitin-40S ribosomal protein S31
+Macromolecule #34: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #35: 40S ribosomal protein S28-A
+Macromolecule #39: 60S ribosomal protein L2-A
+Macromolecule #40: 60S ribosomal protein L3
+Macromolecule #41: 60S ribosomal protein L4-A
+Macromolecule #42: 60S ribosomal protein L5
+Macromolecule #43: 60S ribosomal protein L6-B
+Macromolecule #44: 60S ribosomal protein L7-A
+Macromolecule #45: 60S ribosomal protein L8-A
+Macromolecule #46: 60S ribosomal protein L9-A
+Macromolecule #47: 60S ribosomal protein L10
+Macromolecule #48: 60S ribosomal protein L11-B
+Macromolecule #49: 60S ribosomal protein L13-A
+Macromolecule #50: 60S ribosomal protein L14-A
+Macromolecule #51: 60S ribosomal protein L15-A
+Macromolecule #52: 60S ribosomal protein L16-A
+Macromolecule #53: 60S ribosomal protein L17-A
+Macromolecule #54: 60S ribosomal protein L18-A
+Macromolecule #55: 60S ribosomal protein L19-A
+Macromolecule #56: 60S ribosomal protein L20-A
+Macromolecule #57: 60S ribosomal protein L21-A
+Macromolecule #58: 60S ribosomal protein L22-A
+Macromolecule #59: 60S ribosomal protein L23-A
+Macromolecule #60: 60S ribosomal protein L24-A
+Macromolecule #61: 60S ribosomal protein L25
+Macromolecule #62: 60S ribosomal protein L26-A
+Macromolecule #63: 60S ribosomal protein L27-A
+Macromolecule #64: 60S ribosomal protein L28
+Macromolecule #65: 60S ribosomal protein L29
+Macromolecule #66: 60S ribosomal protein L30
+Macromolecule #67: 60S ribosomal protein L31-A
+Macromolecule #68: 60S ribosomal protein L32
+Macromolecule #69: 60S ribosomal protein L33-A
+Macromolecule #70: 60S ribosomal protein L34-A
+Macromolecule #71: 60S ribosomal protein L35-A
+Macromolecule #72: 60S ribosomal protein L36-A
+Macromolecule #73: 60S ribosomal protein L37-A
+Macromolecule #74: 60S ribosomal protein L38
+Macromolecule #75: 60S ribosomal protein L39
+Macromolecule #76: Ubiquitin-60S ribosomal protein L40
+Macromolecule #77: 60S ribosomal protein L41-B
+Macromolecule #78: 60S ribosomal protein L42-A
+Macromolecule #79: 60S ribosomal protein L43-A
+Macromolecule #81: Elongation factor 3A
+Macromolecule #82: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
|---|---|
Processing | single particle reconstruction |
| Aggregation state | particle |
-
Sample preparation
| Buffer | pH: 6.5 |
|---|---|
| Vitrification | Cryogen name: ETHANE-PROPANE |
-
Electron microscopy
| Microscope | FEI TITAN KRIOS |
|---|---|
| Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 25.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
Movie
Controller
About Yorodumi


Keywords
Authors
Germany, 4 items
Citation
UCSF Chimera























Z
Y
X


































































































Processing

