› 8onz

Electron Microscopy
2.94Å resolution

Chaetomium thermophilum Methionine Aminopeptidase 2 at the 80S ribosome

Released:
DOI: 10.2210/pdb8onz/pdb
PDB entry 8onz coloured by chain, front view.
PDB entry 8onz coloured by chain, side view.
PDB entry 8onz coloured by chain, top view.
Source organism: Thermochaetoides thermophila DSM 1495
Primary publication:
Methionine aminopeptidase 2 and its autoproteolysis product have different binding sites on the ribosome.
Klein MA, Wild K, Kišonaitė M, Sinning I
Nat Commun 15 716 (2024)
PMID: 38267453
Related structures: EMD-17003

Function and Biology Details

Reactions catalysed: 
Dolichyl diphosphooligosaccharide + [protein]-L-asparagine = dolichyl diphosphate + a glycoprotein with the oligosaccharide chain attached by N-beta-D-glycosyl linkage to a protein L-asparagine
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-240159 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (8 distinct):
Ribosomal protein L19 Chain: LR
Molecule details ›
Chain: LR
Length: 2898 amino acids
Theoretical weight: 317.09 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Chaetomium thermophilum var. thermophilum DSM 1495
UniProt:
  • Canonical: G0S9T3 (Residues: 1-2898; Coverage: 100%)
Gene name: CTHT_0047080
Sequence domains:
Large ribosomal subunit protein uL23 N-terminal domain-containing protein Chain: LX
Molecule details ›
Chain: LX
Length: 156 amino acids
Theoretical weight: 17.18 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Chaetomium thermophilum var. thermophilum DSM 1495
UniProt:
  • Canonical: G0S507 (Residues: 1-156; Coverage: 100%)
Gene name: CTHT_0023650
Sequence domains:
KOW domain-containing protein Chain: LY
Molecule details ›
Chain: LY
Length: 138 amino acids
Theoretical weight: 15.57 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Chaetomium thermophilum var. thermophilum DSM 1495
UniProt:
  • Canonical: G0RYN9 (Residues: 1-138; Coverage: 100%)
Gene name: CTHT_0007360
Sequence domains:
dolichyl-diphosphooligosaccharide--protein glycotransferase Chain: Lh
Molecule details ›
Chain: Lh
Length: 935 amino acids
Theoretical weight: 105.17 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Chaetomium thermophilum var. thermophilum DSM 1495
UniProt:
  • Canonical: G0S0D7 (Residues: 1-935; Coverage: 100%)
Gene name: CTHT_0009650
Sequence domains:
60S ribosomal protein L38-like protein Chain: Lk
Molecule details ›
Chain: Lk
Length: 94 amino acids
Theoretical weight: 10.9 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Chaetomium thermophilum var. thermophilum DSM 1495
UniProt:
  • Canonical: G0SG89 (Residues: 1-94; Coverage: 100%)
Gene name: CTHT_0065470
Sequence domains: Ribosomal L38e protein family
Methionine aminopeptidase 2 Chain: A
Molecule details ›
Chain: A
Length: 444 amino acids
Theoretical weight: 48.91 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: G0SEA9 (Residues: 1-444; Coverage: 100%)
Gene name: CTHT_0063100
Sequence domains: Metallopeptidase family M24
28S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 3337 nucleotides
Theoretical weight: 1078.72 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5.8S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 156 nucleotides
Theoretical weight: 50.15 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.94Å
Relevant EMDB volumes: EMD-17003
Expression systems:
  • Chaetomium thermophilum var. thermophilum DSM 1495
  • Spodoptera frugiperda

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