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Open data
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Basic information
Entry | Database: PDB / ID: 6hd7 | |||||||||
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Title | Cryo-EM structure of the ribosome-NatA complex | |||||||||
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![]() | TRANSLATION / N-terminal acetylation / protein modification / ribosome / expansion segments | |||||||||
Function / homology | ![]() N-terminal protein amino acid propionylation / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...N-terminal protein amino acid propionylation / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mitotic sister chromatid cohesion / 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 / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / translational termination / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / macroautophagy / maintenance of translational fidelity / ribosomal large subunit assembly / 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 / mitochondrion / RNA binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Knorr, A.G. / Becker, T. / Beckmann, R. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 215.2 KB | Display | |
Data in CIF | ![]() | 379.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0202MC ![]() 0201C ![]() 0203C ![]() 6hd5C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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#2: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#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) ![]() ![]() |
#5: RNA chain | Mass: 24815.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+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) ![]() ![]() |
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#46: Protein | Mass: 17889.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#50: Protein | Mass: 19753.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ribosome binding subunit / Source: (natural) ![]() ![]() 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) ![]() ![]() |
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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) ![]() ![]() References: UniProt: P07347, N-terminal amino-acid Nalpha-acetyltransferase NatA |
-Protein/peptide / Non-polymers , 2 types, 2 molecules z![](data/chem/img/3HE.gif)
![](data/chem/img/3HE.gif)
#51: Protein/peptide | Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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 |
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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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
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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 |