7naf

Electron Microscopy
3.13Å resolution

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model

Released:

Function and Biology Details

Reactions catalysed:
S-adenosyl-L-methionine + guanosine(2922) in 27S pre-rRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine(2922) in 27S pre-rRNA
S-adenosyl-L-methionine + cytosine(2870) in 25S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(2870) in 25S rRNA
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-220479 (preferred)
Entry contents:
15 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (16 distinct):
Ribosomal RNA-processing protein 17 Chain: 5
Molecule details ›
Chain: 5
Length: 105 amino acids
Theoretical weight: 13.08 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q04031 (Residues: 6-95; Coverage: 36%)
Gene names: RRP17, YDR412W
Sequence domains: Nucleolar protein 12 (25kDa)
Nucleolar complex protein 2 Chain: 8
Molecule details ›
Chain: 8
Length: 39 amino acids
Theoretical weight: 4.75 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P39744 (Residues: 3-41; Coverage: 6%)
Gene names: NOC2, YOR206W, YOX001
Large ribosomal subunit protein uL14A Chain: V
Ribosome biogenesis protein RLP24 Chain: u
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase Chain: w
Nucleolar GTP-binding protein 1 Chain: b
Large ribosomal subunit protein eL31A Chain: d
Large ribosomal subunit protein eL22A Chain: U
Large ribosomal subunit protein eL19A Chain: R
Large ribosomal subunit protein eL30 Chain: c
Large ribosomal subunit protein uL3 Chain: B
UPF0642 protein YBL028C Chain: z
Nuclear GTP-binding protein NUG1 Chain: s
Eukaryotic translation initiation factor 6 Chain: y
25S rRNA (cytosine(2870)-C(5))-methyltransferase Chain: q
25S ribosomal RNA Chain: 1

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
No bound ligands
4 modified residues:

Experiments and Validation Details

Entry percentile scores
Resolution: 3.13Å
Relevant EMDB volumes: EMD-24271