› 8cbj

Electron Microscopy
3.8Å resolution

Cryo-EM structure of Otu2-bound cytoplasmic pre-40S ribosome biogenesis complex

Released:
DOI: 10.2210/pdb8cbj/pdb
PDB entry 8cbj coloured by chain, front view.
PDB entry 8cbj coloured by chain, side view.
PDB entry 8cbj coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2.
Ikeuchi K, Ivic N, Buschauer R, Cheng J, Fröhlich T, Matsuo Y, Berninghausen O, Inada T, Becker T, Beckmann R
OpenAccess logo Nat Commun 14 2730 (2023)
PMID: 37169754
Related structures: EMD-16541

Function and Biology Details

Reactions catalysed: 
ATP + a protein = ADP + a phosphoprotein
4 S-adenosyl-L-methionine + adenine(1779)/adenine(1780) in 18S rRNA = 4 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(1779)/N(6)-dimethyladenine(1780) in 18S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero 39-mer (preferred)
PDBe Complex ID:
PDB-CPX-231662 (preferred)
Entry contents:
38 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (39 distinct):
Small ribosomal subunit protein eS27A Chain: b
Molecule details ›
Chain: b
Length: 82 amino acids
Theoretical weight: 8.89 KDa
Source organism: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P35997 (Residues: 1-82; Coverage: 100%)
Gene names: RPS27A, YKL156W
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS28A Chain: c
Molecule details ›
Chain: c
Length: 67 amino acids
Theoretical weight: 7.61 KDa
Source organism: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: Q3E7X9 (Residues: 1-67; Coverage: 100%)
Gene names: O3600, RPS28A, RPS33, RPS33A, YOR167C
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS14A Chain: d
Small ribosomal subunit protein eS30A Chain: e
Small ribosomal subunit protein RACK1 Chain: g
Pre-rRNA-processing protein PNO1 Chain: h
Essential nuclear protein 1 Chain: i
Protein LTV1 Chain: j
Ribosome biogenesis protein TSR1 Chain: k
Serine/threonine-protein kinase RIO2 Chain: l
Small ribosomal subunit protein uS2A Chain: A
Small ribosomal subunit protein eS1A Chain: B
Small ribosomal subunit protein uS5 Chain: C
Small ribosomal subunit protein uS3 Chain: D
Small ribosomal subunit protein eS4B Chain: E
Small ribosomal subunit protein uS7 Chain: F
Small ribosomal subunit protein eS6B Chain: G
Small ribosomal subunit protein eS7A Chain: H
Small ribosomal subunit protein eS8A Chain: I
Small ribosomal subunit protein uS4A Chain: J
Small ribosomal subunit protein uS17A Chain: L
Small ribosomal subunit protein eS12 Chain: M
Small ribosomal subunit protein uS15 Chain: N
Small ribosomal subunit protein uS11A Chain: O
Small ribosomal subunit protein uS19 Chain: P
Small ribosomal subunit protein uS9A Chain: Q
Small ribosomal subunit protein eS17A Chain: R
Small ribosomal subunit protein uS13A Chain: S
Small ribosomal subunit protein eS19A Chain: T
Small ribosomal subunit protein uS10 Chain: U
Small ribosomal subunit protein eS21A Chain: V
Small ribosomal subunit protein uS8A Chain: W
Small ribosomal subunit protein uS12A Chain: X
Small ribosomal subunit protein eS24A Chain: Y
Small ribosomal subunit protein eS25A Chain: Z
20S-pre-rRNA D-site endonuclease NOB1 Chain: a
Dimethyladenosine transferase Chain: y
OTU domain-containing protein 2 Chain: K
20S pre-ribosomal RNA Chain: 2

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 46 x MG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.8Å
Relevant EMDB volumes: EMD-16541
Expression system: Saccharomyces cerevisiae W303

Quick links

Citations

1 review citation

Roles of the CCR4-Not complex in translation and dynamics of co-translation events.
Collart et al. (2023)
2 other articles