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› 8v83

Electron Microscopy
2.53Å resolution

60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)

Released:
DOI: 10.2210/pdb8v83/pdb
PDB entry 8v83 coloured by chain, front view.
PDB entry 8v83 coloured by chain, side view.
PDB entry 8v83 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae BY4741
Primary publication:
The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
Cruz VE, Weirich CS, Peddada N, Erzberger JP
OpenAccess logo Nat Commun 15 3296 (2024)
PMID: 38632236
Related structures: EMD-43017

Function and Biology Details

Reactions catalysed: 
ATP + H2O = ADP + phosphate + H(+).
cytidine(2870) in 25S rRNA + S-adenosyl-L-methionine =5-methylcytidine(2870) in 25S rRNA + S-adenosyl-L-homocysteine + H(+).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 48-mer (preferred)
PDBe Complex ID:
PDB-CPX-302085 (preferred)
Entry contents:
45 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (48 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
Ribosomal RNA-processing protein 14 Chain: 8
Molecule details ›
Chain: 8
Length: 434 amino acids
Theoretical weight: 50.6 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P36080 (Residues: 1-434; Coverage: 100%)
Gene names: RRP14, YKL082C
Sequence domains:
Ribosome biogenesis protein BRX1 Chain: A
Large ribosomal subunit protein uL3 Chain: B
Large ribosomal subunit protein uL4A Chain: C
ATP-dependent RNA helicase HAS1 Chain: D
Large ribosomal subunit protein eL6A Chain: E
Large ribosomal subunit protein uL30A Chain: F
Large ribosomal subunit protein eL8A Chain: G
Large ribosomal subunit protein uL6A Chain: H
Ribosome biogenesis protein NSA1 Chain: I
rRNA-processing protein EBP2 Chain: J
Proteasome-interacting protein CIC1 Chain: K
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
Protein MAK16 Chain: R
Large ribosomal subunit protein eL20A Chain: S
Ribosomal RNA-processing protein 15 Chain: T
Large ribosomal subunit protein uL14A Chain: V
Ribosome assembly factor MRT4 Chain: W
Large ribosomal subunit protein uL24A Chain: Y
Ribosome biogenesis protein SSF1 Chain: Z
Large ribosomal subunit protein uL1A Chain: a
Nucleolar GTP-binding protein 1 Chain: b
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
Pescadillo homolog Chain: n
Ribosome biogenesis protein 15 Chain: o
25S rRNA (cytosine(2870)-C(5))-methyltransferase Chain: q
Ribosome biogenesis protein NSA2 Chain: r
Ribosome biogenesis protein RLP7 Chain: t
Ribosome biogenesis protein RLP24 Chain: u
Nucleolar protein 16 Chain: v
Ribosomal RNA-processing protein 1 Chain: w
Ribosome production factor 1 Chain: x
Eukaryotic translation initiation factor 6 Chain: y
Saccharomyces cerevisiae S288C 25S ribosomal RNA Chain: 1
Saccharomyces cerevisiae S288C 5.8S ribosomal RNA Chain: 2
Saccharomyces cerevisiae ITS-2 Chain: 6

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 2.53Å
Relevant EMDB volumes: EMD-43017

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