8ONZ

Chaetomium thermophilum Methionine Aminopeptidase 2 at the 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19A [auth LR]2,898Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0047080
UniProt
Find proteins for G0S9T3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0S9T3
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UniProt GroupG0S9T3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25-like proteinB [auth LX]156Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S507 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0S507
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-like proteinC [auth LY]138Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0RYN9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0RYN9
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
dolichyl-diphosphooligosaccharide--protein glycotransferaseD [auth Lh]935Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0009650
EC: 2.4.99.18
UniProt
Find proteins for G0S0D7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0S0D7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38-like proteinE [auth Lk]94Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0065470
UniProt
Find proteins for G0SG89 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 2H [auth A]444Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0063100
UniProt
Find proteins for G0SEA9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 6
MoleculeChains LengthOrganismImage
28S rRNAF [auth 1]3,337Thermochaetoides thermophila DSM 1495
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Entity ID: 7
MoleculeChains LengthOrganismImage
5.8S rRNAG [auth 2]156Thermochaetoides thermophila DSM 1495
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 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