6HD7

Cryo-EM structure of the ribosome-NatA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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: 10.1038/s41594-018-0165-y
  • Structures With Same Primary Citation

  • 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 concer ...

    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. beckmann@genzentrum.lmu.de.



Macromolecules

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-AD92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-AE254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-AG362Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-AI176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-AJ244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-AK256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-AM174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-AN199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-AO138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-AP204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-AR184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-AS186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-AU172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-AV160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-AX137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-AY155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28c149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-Af109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32g130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-Ai121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-Ak100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38m78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39n51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-Ap25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein RPL1r210Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10s221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
N-terminal acetyltransferase A complex subunit NAT1t854Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
N-alpha-acetyltransferase NAT5v176Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.3.1.258
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
nascent polypeptide chainz23Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5H297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-AL191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-AQ199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-AT189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-AW121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25Z142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-Aa127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-Ab136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29d59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30e105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-Ah107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-Aj120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-Al88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40o128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
N-terminal acetyltransferase A complex catalytic subunit ARD1u238Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.3.1.255
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-AC106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3F387Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA13396Saccharomyces cerevisiae

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Entity ID: 2
MoleculeChainsLengthOrganism
5S rRNA3121Saccharomyces cerevisiae

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Entity ID: 3
MoleculeChainsLengthOrganism
5.8S rRNA4158Saccharomyces cerevisiae

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Entity ID: 5
MoleculeChainsLengthOrganism
P-site tRNAB77Saccharomyces cerevisiae

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Entity ID: 4
MoleculeChainsLengthOrganism
tRNAA76Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3HE
Query on 3HE

Download CCD File 
1
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
C15 H23 N O4
YPHMISFOHDHNIV-FSZOTQKASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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 

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