[English] 日本語
Yorodumi- EMDB-30174: Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30174 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) | |||||||||
Map data | Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) | |||||||||
Sample |
| |||||||||
Keywords | Pre-60s / rpl4 / RIBOSOME | |||||||||
Function / homology | Function and homology information protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / PeBoW complex / 7S RNA binding / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / hexon binding ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / PeBoW complex / 7S RNA binding / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / hexon binding / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome binding / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / ATPase activator activity / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / nuclear-transcribed mRNA catabolic process / translational elongation / ribosomal large subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal 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) / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome complex / ribosomal large subunit biogenesis / nuclear periphery / assembly of large subunit precursor of preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cytosolic ribosome assembly / small-subunit processome / macroautophagy / maintenance of translational fidelity / protein catabolic process / rRNA processing / ribosome biogenesis / viral capsid / ribosomal large subunit assembly / protein-macromolecule adaptor activity / ATPase binding / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / host cell nucleus / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||
Authors | Li Y / Wilson DM | |||||||||
Funding support | United States, China, 2 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural insights into assembly of the ribosomal nascent polypeptide exit tunnel. Authors: Daniel M Wilson / Yu Li / Amber LaPeruta / Michael Gamalinda / Ning Gao / John L Woolford / Abstract: The nascent polypeptide exit tunnel (NPET) is a major functional center of 60S ribosomal subunits. However, little is known about how the NPET is constructed during ribosome assembly. We utilized ...The nascent polypeptide exit tunnel (NPET) is a major functional center of 60S ribosomal subunits. However, little is known about how the NPET is constructed during ribosome assembly. We utilized molecular genetics, biochemistry, and cryo-electron microscopy (cryo-EM) to investigate the functions of two NPET-associated proteins, ribosomal protein uL4 and assembly factor Nog1, in NPET assembly. Structures of mutant pre-ribosomes lacking the tunnel domain of uL4 reveal a misassembled NPET, including an aberrantly flexible ribosomal RNA helix 74, resulting in at least three different blocks in 60S assembly. Structures of pre-ribosomes lacking the C-terminal extension of Nog1 demonstrate that this extension scaffolds the tunnel domain of uL4 in the NPET to help maintain stability in the core of pre-60S subunits. Our data reveal that uL4 and Nog1 work together in the maturation of ribosomal RNA helix 74, which is required to ensure proper construction of the NPET and 60S ribosomal subunits. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30174.map.gz | 96.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30174-v30.xml emd-30174.xml | 70.3 KB 70.3 KB | Display Display | EMDB header |
Images | emd_30174.png | 72.3 KB | ||
Filedesc metadata | emd-30174.cif.gz | 16 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30174 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30174 | HTTPS FTP |
-Validation report
Summary document | emd_30174_validation.pdf.gz | 717.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_30174_full_validation.pdf.gz | 716.7 KB | Display | |
Data in XML | emd_30174_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_30174_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30174 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30174 | HTTPS FTP |
-Related structure data
Related structure data | 7btbMC 7bt6C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_30174.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3734 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisi...
+Supramolecule #1: Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisi...
+Macromolecule #1: 60S ribosomal protein L13-A
+Macromolecule #2: 60S ribosomal protein L28
+Macromolecule #3: 60S ribosomal protein L2-A
+Macromolecule #4: 60S ribosomal protein L3
+Macromolecule #5: 60S ribosomal protein L4-A
+Macromolecule #6: 60S ribosomal protein L5
+Macromolecule #7: 60S ribosomal protein L6-A
+Macromolecule #8: 60S ribosomal protein L7-A
+Macromolecule #9: 60S ribosomal protein L8-A
+Macromolecule #10: 60S ribosomal protein L9-A
+Macromolecule #11: 60S ribosomal protein L11-A
+Macromolecule #12: Proteasome-interacting protein CIC1
+Macromolecule #13: 60S ribosomal protein L14-A
+Macromolecule #14: 60S ribosomal protein L15-A
+Macromolecule #15: 60S ribosomal protein L16-A
+Macromolecule #16: 60S ribosomal protein L17-A
+Macromolecule #17: 60S ribosomal protein L18-A
+Macromolecule #18: 60S ribosomal protein L19-A
+Macromolecule #19: 60S ribosomal protein L20-A
+Macromolecule #20: 60S ribosomal protein L21-A
+Macromolecule #21: 60S ribosomal protein L22-A
+Macromolecule #22: 60S ribosomal protein L23-A
+Macromolecule #23: Ribosome assembly factor MRT4
+Macromolecule #24: 60S ribosomal protein L25
+Macromolecule #25: 60S ribosomal protein L26-A
+Macromolecule #26: 60S ribosomal protein L27-A
+Macromolecule #27: Nucleolar GTP-binding protein 1
+Macromolecule #28: 60S ribosomal protein L30
+Macromolecule #29: 60S ribosomal protein L31-A
+Macromolecule #30: 60S ribosomal protein L32
+Macromolecule #31: 60S ribosomal protein L33-A
+Macromolecule #32: 60S ribosomal protein L34-A
+Macromolecule #33: 60S ribosomal protein L35-A
+Macromolecule #34: 60S ribosomal protein L36-A
+Macromolecule #35: 60S ribosomal protein L37-A
+Macromolecule #36: 60S ribosomal protein L38
+Macromolecule #37: Nucleolar GTP-binding protein 2
+Macromolecule #38: Pescadillo homolog
+Macromolecule #39: Ribosome biogenesis protein 15
+Macromolecule #40: 60S ribosomal protein L43-A
+Macromolecule #41: Ribosome biogenesis protein NOP53
+Macromolecule #42: Ribosome biogenesis protein NSA2
+Macromolecule #43: Ribosome biogenesis protein RLP7
+Macromolecule #44: Ribosome biogenesis protein RLP24
+Macromolecule #45: Ribosome biogenesis protein RPF2
+Macromolecule #46: Regulator of ribosome biosynthesis
+Macromolecule #47: Ribosome assembly protein 4
+Macromolecule #48: Eukaryotic translation initiation factor 6
+Macromolecule #49: UPF0642 protein YBL028C
+Macromolecule #50: RDN25-1 rRNA
+Macromolecule #51: RDN5.8-1 rRNA
+Macromolecule #52: RDN5-2 rRNA
+Macromolecule #53: ITS2-1 miscRNA
+Macromolecule #54: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #55: MAGNESIUM ION
+Macromolecule #56: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.9 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 |
-Image processing
Startup model | Type of model: EMDB MAP |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47025 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |