7r7a

Electron Microscopy
3.04Å resolution

State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model

Released:

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
PDBe Complex ID:
PDB-CPX-216271 (preferred)
Entry contents:
54 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (57 distinct):
60S ribosomal subunit assembly/export protein LOC1 Chain: 7
Molecule details ›
Chain: 7
Length: 204 amino acids
Theoretical weight: 23.65 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P43586 (Residues: 1-204; Coverage: 100%)
Gene names: LOC1, YFR001W
Ribosome biogenesis protein BRX1 Chain: A
Molecule details ›
Chain: A
Length: 291 amino acids
Theoretical weight: 33.59 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q08235 (Residues: 1-291; Coverage: 100%)
Gene names: BRX1, YOL077C
Sequence domains: Brix domain
Large ribosomal subunit protein uL3 Chain: B
Large ribosomal subunit protein uL4A Chain: C
Large ribosomal subunit protein eL6A Chain: E
Large ribosomal subunit protein uL30A Chain: F
Large ribosomal subunit protein uL6A Chain: H
rRNA-processing protein EBP2 Chain: J
Large ribosomal subunit protein eL13A Chain: L
Large ribosomal subunit protein eL14A Chain: M
Large ribosomal subunit protein eL15A Chain: N
Large ribosomal subunit protein uL13A Chain: O
Large ribosomal subunit protein uL22A Chain: P
Large ribosomal subunit protein eL18A Chain: Q
Large ribosomal subunit protein eL20A Chain: S
Large ribosomal subunit protein eL21A Chain: T
Ribosome assembly factor MRT4 Chain: W
Large ribosomal subunit protein uL23 Chain: X
Large ribosomal subunit protein uL24A Chain: Y
Nucleolar GTP-binding protein 1 Chain: b
Large ribosomal subunit protein eL31A Chain: d
Large ribosomal subunit protein eL32 Chain: e
Large ribosomal subunit protein eL33A Chain: f
Large ribosomal subunit protein uL29A Chain: h
Large ribosomal subunit protein eL36A Chain: i
Large ribosomal subunit protein eL37A Chain: j
60S ribosome subunit biogenesis protein NIP7 Chain: l
Ribosome biogenesis protein ERB1 Chain: m
25S rRNA (cytosine(2870)-C(5))-methyltransferase Chain: q
Ribosome biogenesis protein NSA2 Chain: r
Nuclear GTP-binding protein NUG1 Chain: s
Ribosome biogenesis protein RLP24 Chain: u
Nucleolar protein 16 Chain: v
Eukaryotic translation initiation factor 6 Chain: y
UPF0642 protein YBL028C Chain: z
Nucleolar complex protein 2 Chain: 8
Nucleolar complex-associated protein 3 Chain: I
Proteasome-interacting protein CIC1 Chain: K
Large ribosomal subunit protein uL14A Chain: V
Large ribosomal subunit protein eL19A Chain: R
Large ribosomal subunit protein eL8A Chain: G
Large ribosomal subunit protein eL27A Chain: Z
Large ribosomal subunit protein eL22A Chain: U
Large ribosomal subunit protein eL30 Chain: c
Large ribosomal subunit protein eL34A Chain: g
Large ribosomal subunit protein eL38 Chain: k
Pescadillo homolog Chain: n
Ribosome biogenesis protein YTM1 Chain: p
Ribosome biogenesis protein RLP7 Chain: t
ATP-dependent RNA helicase HAS1 Chain: D
Ribosome biogenesis protein 15 Chain: o
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase Chain: w
Large ribosomal subunit protein uL1A Chain: a
ATP-dependent rRNA helicase SPB4 Chain: x
25S ribosomal RNA Chain: 1
5.8S ribosomal RNA Chain: 2
5.8S ribosomal RNA gene and internal transcribed spacer 2 Chain: 6

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.04Å
Relevant EMDB volumes: EMD-24296