9FPZ | pdb_00009fpz

Human NatA-MAP2 80S ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Multi-protein assemblies orchestrate co-translational enzymatic processing on the human ribosome.

Klein, M.Wild, K.Sinning, I.

(2024) Nat Commun 15: 7681-7681

  • DOI: https://doi.org/10.1038/s41467-024-51964-9
  • Primary Citation of Related Structures:  
    9FPZ, 9FQ0

  • PubMed Abstract: 

    Nascent chains undergo co-translational enzymatic processing as soon as their N-terminus becomes accessible at the ribosomal polypeptide tunnel exit (PTE). In eukaryotes, N-terminal methionine excision (NME) by Methionine Aminopeptidases (MAP1 and MAP2), and N-terminal acetylation (NTA) by N-Acetyl-Transferase A (NatA), is the most common combination of subsequent modifications carried out on the 80S ribosome. How these enzymatic processes are coordinated in the context of a rapidly translating ribosome has remained elusive. Here, we report two cryo-EM structures of multi-enzyme complexes assembled on vacant human 80S ribosomes, indicating two routes for NME-NTA. Both assemblies form on the 80S independent of nascent chain substrates. Irrespective of the route, NatA occupies a non-intrusive 'distal' binding site on the ribosome which does not interfere with MAP1 or MAP2 binding nor with most other ribosome-associated factors (RAFs). NatA can partake in a coordinated, dynamic assembly with MAP1 through the hydra-like chaperoning function of the abundant Nascent Polypeptide-Associated Complex (NAC). In contrast to MAP1, MAP2 completely covers the PTE and is thus incompatible with NAC and MAP1 recruitment. Together, our data provide the structural framework for the coordinated orchestration of NME and NTA in protein biogenesis.


  • Organizational Affiliation
    • Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 10A [auth 2]171Homo sapiensMutation(s): 0 
Gene Names: NAA10ARD1ARD1ATE2
EC: 2.3.1.255
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PHAROS:  P41227
GTEx:  ENSG00000102030 
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UniProt GroupP41227
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 2C [auth A]484Homo sapiensMutation(s): 0 
Gene Names: METAP2MNPEPP67EIF2
EC: 3.4.11.18
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PHAROS:  P50579
GTEx:  ENSG00000111142 
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UniProt GroupP50579
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 15, NatA auxiliary subunitD [auth B]840Homo sapiensMutation(s): 0 
Gene Names: NAA15GA19NARG1NATHTBDN100
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PHAROS:  Q9BXJ9
GTEx:  ENSG00000164134 
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UniProt GroupQ9BXJ9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4F [auth LC]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6G [auth LE]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38H [auth Lk]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24I [auth LY]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35J [auth Lh]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aK [auth LX]156Homo sapiensMutation(s): 0 
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PHAROS:  P62750
GTEx:  ENSG00000198242 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19L [auth LR]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28M [auth Lr]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 2
MoleculeChains LengthOrganismImage
5.8S rRNA (58-MER)B [auth 8]58Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
28S rRNAE [auth 1]5,070Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 2.0: 2024-10-02
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary