6HD5

Cryo-EM structure of the ribosome-NatA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation.

Knorr, A.G.Schmidt, C.Tesina, P.Berninghausen, O.Becker, T.Beatrix, B.Beckmann, R.

(2019) Nat Struct Mol Biol 26: 35-39

  • DOI: https://doi.org/10.1038/s41594-018-0165-y
  • Primary Citation of Related Structures:  
    6HD5, 6HD7

  • PubMed 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. 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.


  • Organizational Affiliation

    Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase A complex subunit NAT1A [auth t]854Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P12945 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P12945 
Go to UniProtKB:  P12945
Entity Groups  
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UniProt GroupP12945
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase A complex catalytic subunit ARD1B [auth u]238Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.3.1.255
UniProt
Find proteins for P07347 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07347 
Go to UniProtKB:  P07347
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UniProt GroupP07347
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase NAT5C [auth v]176Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.3.1.258
UniProt
Find proteins for Q08689 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08689 
Go to UniProtKB:  Q08689
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08689
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK1721
German Research FoundationGermanyFOR1805

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-16
    Changes: Data collection, Database references