+Open data
-Basic information
Entry | Database: PDB / ID: 6hd7 | |||||||||
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Title | Cryo-EM structure of the ribosome-NatA complex | |||||||||
Components |
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Keywords | TRANSLATION / N-terminal acetylation / protein modification / ribosome / expansion segments | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Knorr, A.G. / Becker, T. / Beckmann, R. | |||||||||
Funding support | Germany, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6hd7.cif.gz | 3.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6hd7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6hd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hd7_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6hd7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6hd7_validation.xml.gz | 215.2 KB | Display | |
Data in CIF | 6hd7_validation.cif.gz | 379.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/6hd7 ftp://data.pdbj.org/pub/pdb/validation_reports/hd/6hd7 | HTTPS FTP |
-Related structure data
Related structure data | 0202MC 0201C 0203C 6hd5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 5 types, 5 molecules 134AB
#1: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: REF: 831416132 |
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#2: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
#3: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1398978137 |
#4: RNA chain | Mass: 24378.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The A-site tRNA was modeled based on an E. coli tRNA-Lys Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
#5: RNA chain | Mass: 24815.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
+60S ribosomal protein ... , 40 types, 40 molecules CDEFGHIJKLMNOPQRSTUVWXYZabcdef...
-Protein , 3 types, 3 molecules orv
#44: Protein | Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CH08 |
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#46: Protein | Mass: 17889.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
#50: Protein | Mass: 19753.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ribosome binding subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: Q08689, N-terminal methionine Nalpha-acetyltransferase NatE |
-N-terminal acetyltransferase A complex ... , 2 types, 2 molecules tu
#48: Protein | Mass: 99050.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ribosome binding subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12945 |
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#49: Protein | Mass: 27635.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: catalytic subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P07347, N-terminal amino-acid Nalpha-acetyltransferase NatA |
-Protein/peptide / Non-polymers , 2 types, 2 molecules z
#51: Protein/peptide | Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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#52: Chemical | ChemComp-3HE / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 262507 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |