8ONY

Human Methionine Aminopeptidase 2 at the 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Methionine aminopeptidase 2 and its autoproteolysis product have different binding sites on the ribosome.

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

(2024) Nat Commun 15: 716-716

  • DOI: https://doi.org/10.1038/s41467-024-44862-7
  • Primary Citation of Related Structures:  
    8ONX, 8ONY, 8ONZ, 8OO0

  • PubMed Abstract: 

    Excision of the initiator methionine is among the first co-translational processes that occur at the ribosome. While this crucial step in protein maturation is executed by two types of methionine aminopeptidases in eukaryotes (MAP1 and MAP2), additional roles in disease and translational regulation have drawn more attention to MAP2. Here, we report several cryo-EM structures of human and fungal MAP2 at the 80S ribosome. Irrespective of nascent chains, MAP2 can occupy the tunnel exit. On nascent chain displaying ribosomes, the MAP2-80S interaction is highly dynamic and the MAP2-specific N-terminal extension engages in stabilizing interactions with the long rRNA expansion segment ES27L. Loss of this extension by autoproteolytic cleavage impedes interactions at the tunnel, while promoting MAP2 to enter the ribosomal A-site, where it engages with crucial functional centers of translation. These findings reveal that proteolytic remodeling of MAP2 severely affects ribosome binding, and set the stage for targeted functional studies.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38B [auth Lk]70Homo sapiensMutation(s): 0 
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Find proteins for P63173 (Homo sapiens)
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PHAROS:  P63173
GTEx:  ENSG00000172809 
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UniProt GroupP63173
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26C [auth LY]145Homo sapiensMutation(s): 0 
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Find proteins for P61254 (Homo sapiens)
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PHAROS:  P61254
GTEx:  ENSG00000161970 
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UniProt GroupP61254
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35D [auth Lh]123Homo sapiensMutation(s): 0 
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Find proteins for P42766 (Homo sapiens)
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PHAROS:  P42766
GTEx:  ENSG00000136942 
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UniProt GroupP42766
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aE [auth LX]156Homo sapiensMutation(s): 0 
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Find proteins for P62750 (Homo sapiens)
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PHAROS:  P62750
GTEx:  ENSG00000198242 
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UniProt GroupP62750
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19F [auth LR]196Homo sapiensMutation(s): 0 
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Find proteins for P84098 (Homo sapiens)
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PHAROS:  P84098
GTEx:  ENSG00000108298 
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UniProt GroupP84098
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 2H [auth A]478Homo sapiensMutation(s): 0 
Gene Names: METAP2MNPEPP67EIF2
EC: 3.4.11.18
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Find proteins for P50579 (Homo sapiens)
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GTEx:  ENSG00000111142 
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UniProt GroupP50579
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Entity ID: 1
MoleculeChains LengthOrganismImage
28S rRNAA [auth 5]5,070Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
5.8S rRNAG [auth 8]157Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19_4092:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySI 586-6

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release