7nad

Electron Microscopy
3.04Å resolution

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement 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
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 26-mer (preferred)
PDBe Complex ID:
PDB-CPX-220475 (preferred)
Entry contents:
24 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (26 distinct):
Ribosomal RNA-processing protein 17 Chain: 5
Molecule details ›
Chain: 5
Length: 235 amino acids
Theoretical weight: 28.03 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q04031 (Residues: 1-235; Coverage: 100%)
Gene names: RRP17, YDR412W
Sequence domains: Nucleolar protein 12 (25kDa)
Nucleolar complex protein 2 Chain: 8
Molecule details ›
Chain: 8
Length: 710 amino acids
Theoretical weight: 81.72 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P39744 (Residues: 1-710; Coverage: 100%)
Gene names: NOC2, YOR206W, YOX001
Sequence domains: Noc2p family
Large ribosomal subunit protein uL3 Chain: B
Large ribosomal subunit protein eL8A Chain: G
Nucleolar complex-associated protein 3 Chain: I
Large ribosomal subunit protein uL22A Chain: P
Large ribosomal subunit protein eL19A Chain: R
Large ribosomal subunit protein eL22A Chain: U
Large ribosomal subunit protein uL14A Chain: V
Large ribosomal subunit protein uL23 Chain: X
Large ribosomal subunit protein eL27A Chain: Z
Nucleolar GTP-binding protein 1 Chain: b
Large ribosomal subunit protein eL30 Chain: c
Large ribosomal subunit protein eL31A Chain: d
Large ribosomal subunit protein eL34A Chain: g
Large ribosomal subunit protein eL38 Chain: k
Ribosome biogenesis protein ERB1 Chain: m
Pescadillo homolog Chain: n
Ribosome biogenesis protein YTM1 Chain: p
Ribosome biogenesis protein RLP7 Chain: t
Ribosome biogenesis protein RLP24 Chain: u
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase Chain: w
Large ribosomal subunit protein eL37A Chain: j
ATP-dependent rRNA helicase SPB4 Chain: x
25S ribosomal RNA Chain: 1
5.8S ribosomal RNA Chain: 2

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.04Å
Relevant EMDB volumes: EMD-24270