9GJ5 | pdb_00009gj5

Human 80S ribosome in complex with NatA in distal position and Ebp1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

NatA engages in multi-factor complexes at the ribosomal polypeptide tunnel exit.

Klein, M.Wild, K.McTiernan, N.Arnesen, T.Sinning, I.

(2026) Nat Commun 17: 884-884

  • DOI: https://doi.org/10.1038/s41467-026-68787-5
  • Primary Citation Related Structures: 
    9GJ5, 9GJ6

  • PubMed Abstract: 

    N-terminal acetylation (NTA) is the most common protein modification in eukaryotes, playing a crucial role in proteostasis. Almost 40% of the human proteome is acetylated co-translationally by the NatA complex, which requires prior N-terminal methionine excision (NME). Recently, NatA was shown to form multi-enzyme complexes with MAP1/NAC or MAP2, combining the capabilities of NME and NTA into a single complex. Here, we show that NatA can also form ribosome-independent assemblies with several ribosome associated factors (RAFs). At the ribosome, NatA can form a ternary complex with the abundant pseudoenzyme Ebp1 or a second copy of NatA, which can be coordinated from a different binding site with closer access to a potential substrate. Further, we identify a conserved binding site on NatA, which can be accessed by four RAFs - Ebp1, NAC, Naa10 and HypK, allowing the formation of different multi-factor complexes at the ribosomal tunnel exit. Therefore, our data suggest that NatA constitutes an interaction hub, and contributes to the coordination of co-translational protein maturation.


  • Organizational Affiliation
    • Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 2,031.4 kDa 
  • Atom Count: 29,428 
  • Modeled Residue Count: 3,030 
  • Deposited Residue Count: 8,172 
  • Unique protein chains: 11
  • Unique nucleic acid chains: 2

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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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 15, NatA auxiliary subunitC [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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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L4E [auth LC]427Homo sapiensMutation(s): 0 
Gene Names: RPL4RPL1
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PHAROS:  P36578
GTEx:  ENSG00000174444 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6F [auth LE]288Homo sapiensMutation(s): 0 
Gene Names: RPL6TXREB1
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PHAROS:  Q02878
GTEx:  ENSG00000089009 
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UniProt GroupQ02878
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L38G [auth Lk]70Homo sapiensMutation(s): 0 
Gene Names: RPL38
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Find proteins for P63173 (Homo sapiens)
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PHAROS:  P63173
GTEx:  ENSG00000172809 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24H [auth LY]144Homo sapiensMutation(s): 0 
Gene Names: RPL26
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PHAROS:  P61254
GTEx:  ENSG00000161970 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35I [auth Lh]122Homo sapiensMutation(s): 0 
Gene Names: RPL35
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Find proteins for P42766 (Homo sapiens)
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PHAROS:  P42766
GTEx:  ENSG00000136942 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aJ [auth LX]156Homo sapiensMutation(s): 0 
Gene Names: RPL23A
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Find proteins for P62750 (Homo sapiens)
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PHAROS:  P62750
GTEx:  ENSG00000198242 
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L19K [auth LR]196Homo sapiensMutation(s): 0 
Gene Names: RPL19
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PHAROS:  P84098
GTEx:  ENSG00000108298 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L28L [auth Lr]137Homo sapiensMutation(s): 0 
Gene Names: RPL28
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PHAROS:  P46779
GTEx:  ENSG00000108107 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Proliferation-associated protein 2G4M [auth A]394Homo sapiensMutation(s): 0 
Gene Names: PA2G4EBP1
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Find proteins for Q9UQ80 (Homo sapiens)
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PHAROS:  Q9UQ80
GTEx:  ENSG00000170515 
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UniProt GroupQ9UQ80
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
5.8S rRNAB [auth 8]157Homo sapiens
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
28S rRNAD [auth 1]5,070Homo sapiens
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KGN

Query on KGN



Download:Ideal Coordinates CCD File
N [auth B]D-chiro inositol hexakisphosphate
C6 H18 O24 P6
IMQLKJBTEOYOSI-LKPKBOIGSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.61 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: 2026-02-18
    Type: Initial release
  • Version 1.1: 2026-06-03
    Changes: Data collection, Database references