+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0202 | |||||||||
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Title | Cryo-EM structure of the ribosome-NatA complex | |||||||||
Map data | Ribosome-NatA complex aligned on the ribosome and filtered according to local resolution. | |||||||||
Sample |
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Function / homology | Function and homology information peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / peptide alpha-N-acetyltransferase activity / pre-mRNA 5'-splice site binding / mitotic sister chromatid cohesion / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide ...peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / peptide alpha-N-acetyltransferase activity / pre-mRNA 5'-splice site binding / mitotic sister chromatid cohesion / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / translational termination / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Knorr AG / Becker T / Berninghausen O / Beckmann R | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation. Authors: Alexandra G Knorr / Christian Schmidt / Petr Tesina / Otto Berninghausen / Thomas Becker / Birgitta Beatrix / Roland Beckmann / Abstract: The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. ...The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. Nevertheless, it is unclear how these enzymes act in concert with the translating ribosome. Here, we report the structure of a native ribosome-NatA complex from Saccharomyces cerevisiae. NatA (comprising Naa10, Naa15 and Naa50) displays a unique mode of ribosome interaction by contacting eukaryotic-specific ribosomal RNA expansion segments in three out of four binding patches. Thereby, NatA is dynamically positioned directly underneath the ribosomal exit tunnel to facilitate modification of the emerging nascent peptide chain. Methionine amino peptidases, but not chaperones or signal recognition particle, would be able to bind concomitantly. This work assigns a function to the hitherto enigmatic ribosomal RNA expansion segments and provides mechanistic insights into co-translational protein maturation by N-terminal acetylation. | |||||||||
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_0202.map.gz | 162.2 MB | EMDB map data format | |
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Header (meta data) | emd-0202-v30.xml emd-0202.xml | 70.9 KB 70.9 KB | Display Display | EMDB header |
Images | emd_0202.png | 192.9 KB | ||
Others | emd_0202_additional.map.gz | 264.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0202 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0202 | HTTPS FTP |
-Validation report
Summary document | emd_0202_validation.pdf.gz | 247.7 KB | Display | EMDB validaton report |
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Full document | emd_0202_full_validation.pdf.gz | 246.8 KB | Display | |
Data in XML | emd_0202_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0202 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0202 | HTTPS FTP |
-Related structure data
Related structure data | 6hd7MC 0201C 0203C 6hd5C 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_0202.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ribosome-NatA complex aligned on the ribosome and filtered according to local resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Ribosome-NatA complex aligned on the ribosome, postprocessed unfiltered...
File | emd_0202_additional.map | ||||||||||||
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Annotation | Ribosome-NatA complex aligned on the ribosome, postprocessed unfiltered map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ribosome-NatA complex
+Supramolecule #1: Ribosome-NatA complex
+Supramolecule #2: 60S ribosomal subunit
+Supramolecule #3: N-terminal acetyl transferase A
+Macromolecule #1: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), m...
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #4: tRNA
+Macromolecule #5: P-site tRNA
+Macromolecule #6: 60S ribosomal protein L42-A
+Macromolecule #7: 60S ribosomal protein L43-A
+Macromolecule #8: 60S ribosomal protein L2-A
+Macromolecule #9: 60S ribosomal protein L3
+Macromolecule #10: 60S ribosomal protein L4-A
+Macromolecule #11: 60S ribosomal protein L5
+Macromolecule #12: 60S ribosomal protein L6-A
+Macromolecule #13: 60S ribosomal protein L7-A
+Macromolecule #14: 60S ribosomal protein L8-A
+Macromolecule #15: 60S ribosomal protein L9-A
+Macromolecule #16: 60S ribosomal protein L11-A
+Macromolecule #17: 60S ribosomal protein L13-A
+Macromolecule #18: 60S ribosomal protein L14-A
+Macromolecule #19: 60S ribosomal protein L15-A
+Macromolecule #20: 60S ribosomal protein L16-A
+Macromolecule #21: 60S ribosomal protein L17-A
+Macromolecule #22: 60S ribosomal protein L18-A
+Macromolecule #23: 60S ribosomal protein L19-A
+Macromolecule #24: 60S ribosomal protein L20-A
+Macromolecule #25: 60S ribosomal protein L21-A
+Macromolecule #26: 60S ribosomal protein L22-A
+Macromolecule #27: 60S ribosomal protein L23-A
+Macromolecule #28: 60S ribosomal protein L24-A
+Macromolecule #29: 60S ribosomal protein L25
+Macromolecule #30: 60S ribosomal protein L26-A
+Macromolecule #31: 60S ribosomal protein L27-A
+Macromolecule #32: 60S ribosomal protein L28
+Macromolecule #33: 60S ribosomal protein L29
+Macromolecule #34: 60S ribosomal protein L30
+Macromolecule #35: 60S ribosomal protein L31-A
+Macromolecule #36: 60S ribosomal protein L32
+Macromolecule #37: 60S ribosomal protein L33-A
+Macromolecule #38: 60S ribosomal protein L34-A
+Macromolecule #39: 60S ribosomal protein L35-A
+Macromolecule #40: 60S ribosomal protein L36-A
+Macromolecule #41: 60S ribosomal protein L37-A
+Macromolecule #42: 60S ribosomal protein L38
+Macromolecule #43: 60S ribosomal protein L39
+Macromolecule #44: Ubiquitin-60S ribosomal protein L40
+Macromolecule #45: 60S ribosomal protein L41-A
+Macromolecule #46: ribosomal protein RPL1
+Macromolecule #47: 60S ribosomal protein L10
+Macromolecule #48: N-terminal acetyltransferase A complex subunit NAT1
+Macromolecule #49: N-terminal acetyltransferase A complex catalytic subunit ARD1
+Macromolecule #50: N-alpha-acetyltransferase NAT5
+Macromolecule #51: nascent polypeptide chain
+Macromolecule #52: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 262507 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6hd7: |