8ONX | pdb_00008onx

High resolution structure of Chaetomium thermophilum MAP2

• PDB DOI: https://doi.org/10.2210/pdb8ONX/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Thermochaetoides thermophila
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-04-04 Released: 2024-02-14 
• Deposition Author(s): Klein, M.A., Wild, K., Kisonaite, M., Sinning, I.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: in silico

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

• PubMed: 38267453 
• DOI: https://doi.org/10.1038/s41467-024-44862-7
• Primary Citation 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.

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Organizational Affiliation: 
• Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.81 kDa 
• Atom Count: 3,509 
• Modeled Residue Count: 371 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase 2	A	376	Thermochaetoides thermophila	Mutation(s): 0  Gene Names: CTHT_0063100 EC: 3.4.11.18
UniProt
Find proteins for G0SEA9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SEA9  Go to UniProtKB:  G0SEA9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.938	α = 90
b = 73.806	β = 90
c = 82.049	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Klein, M.A., Wild, K., Kisonaite, M., Sinning, I.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SI 586-6

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release