› 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 + H(2)O = ADP + phosphate
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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 48-mer (preferred)
PDBe Complex ID:
PDB-CPX-272348 (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
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
Molecule details ›
Chain: B
Length: 387 amino acids
Theoretical weight: 43.85 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P14126 (Residues: 1-387; Coverage: 100%)
Gene names: MAK8, RPL3, TCM1, YOR063W, YOR29-14
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4A Chain: C
Molecule details ›
Chain: C
Length: 362 amino acids
Theoretical weight: 39.16 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P10664 (Residues: 1-362; Coverage: 100%)
Gene names: RPL2, RPL2A, RPL4A, YBR0315, YBR031W
Sequence domains:
ATP-dependent RNA helicase HAS1 Chain: D
Molecule details ›
Chain: D
Length: 505 amino acids
Theoretical weight: 56.8 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q03532 (Residues: 1-505; Coverage: 100%)
Gene names: HAS1, YMR290C
Sequence domains:
Large ribosomal subunit protein eL6A Chain: E
Molecule details ›
Chain: E
Length: 176 amino acids
Theoretical weight: 20 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q02326 (Residues: 1-176; Coverage: 100%)
Gene names: RPL17A, RPL6A, YL16A, YML073C
Sequence domains: Ribosomal protein L6e
Large ribosomal subunit protein uL30A Chain: F
Molecule details ›
Chain: F
Length: 244 amino acids
Theoretical weight: 27.69 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05737 (Residues: 1-244; Coverage: 100%)
Gene names: RPL6A, RPL7A, RPL8A, YGL076C, YL8A
Sequence domains:
Large ribosomal subunit protein eL8A Chain: G
Molecule details ›
Chain: G
Length: 256 amino acids
Theoretical weight: 28.18 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P17076 (Residues: 1-256; Coverage: 100%)
Gene names: MAK7, RPL4A, RPL8A, YHL033C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL6A Chain: H
Molecule details ›
Chain: H
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05738 (Residues: 1-191; Coverage: 100%)
Gene names: RPL8A, RPL9, RPL9A, YGL147C
Sequence domains: Ribosomal protein L6
Ribosome biogenesis protein NSA1 Chain: I
Molecule details ›
Chain: I
Length: 463 amino acids
Theoretical weight: 51.98 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P53136 (Residues: 1-463; Coverage: 100%)
Gene names: G2990, NSA1, YGL111W
rRNA-processing protein EBP2 Chain: J
Molecule details ›
Chain: J
Length: 427 amino acids
Theoretical weight: 49.84 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P36049 (Residues: 1-427; Coverage: 100%)
Gene names: EBP2, YKL172W, YKL636
Sequence domains: Eukaryotic rRNA processing protein EBP2
Proteasome-interacting protein CIC1 Chain: K
Molecule details ›
Chain: K
Length: 376 amino acids
Theoretical weight: 42.6 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P38779 (Residues: 1-376; Coverage: 100%)
Gene names: CIC1, NSA3, YHR052W
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein eL13A Chain: L
Molecule details ›
Chain: L
Length: 199 amino acids
Theoretical weight: 22.6 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q12690 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13A, YDL082W
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14A Chain: M
Molecule details ›
Chain: M
Length: 138 amino acids
Theoretical weight: 15.2 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P36105 (Residues: 1-138; Coverage: 100%)
Gene names: RPL14A, YKL006W, YKL153
Sequence domains:
Large ribosomal subunit protein eL15A Chain: N
Molecule details ›
Chain: N
Length: 204 amino acids
Theoretical weight: 24.48 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05748 (Residues: 1-204; Coverage: 100%)
Gene names: RPL10A, RPL13A, RPL15A, YL10A, YLR029C
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL13A Chain: O
Molecule details ›
Chain: O
Length: 199 amino acids
Theoretical weight: 22.25 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P26784 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13, RPL16A, RPL21A, YIL133C
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL22A Chain: P
Molecule details ›
Chain: P
Length: 184 amino acids
Theoretical weight: 20.59 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05740 (Residues: 1-184; Coverage: 100%)
Gene names: RPL17, RPL17A, RPL20A, YKL180W
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL18A Chain: Q
Molecule details ›
Chain: Q
Length: 186 amino acids
Theoretical weight: 20.61 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX49 (Residues: 1-186; Coverage: 100%)
Gene names: RP28A, RPL18A, YOL120C
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Protein MAK16 Chain: R
Molecule details ›
Chain: R
Length: 306 amino acids
Theoretical weight: 35.75 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P10962 (Residues: 1-306; Coverage: 100%)
Gene names: MAK16, YAL025C
Sequence domains:
Large ribosomal subunit protein eL20A Chain: S
Molecule details ›
Chain: S
Length: 172 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX23 (Residues: 1-172; Coverage: 100%)
Gene names: RPL18A, RPL18A2, RPL20A, YM9408.04C, YMR242C
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Ribosomal RNA-processing protein 15 Chain: T
Molecule details ›
Chain: T
Length: 250 amino acids
Theoretical weight: 28.27 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q06511 (Residues: 1-250; Coverage: 100%)
Gene names: RRP15, YPR143W
Sequence domains: Rrp15p
Large ribosomal subunit protein uL14A Chain: V
Molecule details ›
Chain: V
Length: 137 amino acids
Theoretical weight: 14.49 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX41 (Residues: 1-137; Coverage: 100%)
Gene names: RPL17A, RPL17AA, RPL23A, YBL0713, YBL087C
Sequence domains: Ribosomal protein L14p/L23e
Ribosome assembly factor MRT4 Chain: W
Molecule details ›
Chain: W
Length: 236 amino acids
Theoretical weight: 27.1 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P33201 (Residues: 1-236; Coverage: 100%)
Gene names: MRT4, YKL009W, YKL160
Sequence domains:
Large ribosomal subunit protein uL24A Chain: Y
Molecule details ›
Chain: Y
Length: 127 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05743 (Residues: 1-127; Coverage: 100%)
Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:
Ribosome biogenesis protein SSF1 Chain: Z
Molecule details ›
Chain: Z
Length: 453 amino acids
Theoretical weight: 51.86 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P38789 (Residues: 1-453; Coverage: 100%)
Gene names: SSF1, YHR066W
Sequence domains: Brix domain
Large ribosomal subunit protein uL1A Chain: a
Molecule details ›
Chain: a
Length: 217 amino acids
Theoretical weight: 24.52 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX43 (Residues: 1-217; Coverage: 100%)
Gene names: RPL1A, SSM1, SSM1A, YPL220W
Sequence domains: Ribosomal protein L1p/L10e family
Nucleolar GTP-binding protein 1 Chain: b
Molecule details ›
Chain: b
Length: 647 amino acids
Theoretical weight: 74.53 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q02892 (Residues: 1-647; Coverage: 100%)
Gene names: LPG15W, NOG1, YPL093W
Sequence domains:
Large ribosomal subunit protein eL32 Chain: e
Molecule details ›
Chain: e
Length: 130 amino acids
Theoretical weight: 14.81 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P38061 (Residues: 1-130; Coverage: 100%)
Gene names: RPL32, YBL0838, YBL092W
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL33A Chain: f
Molecule details ›
Chain: f
Length: 107 amino acids
Theoretical weight: 12.18 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05744 (Residues: 1-107; Coverage: 100%)
Gene names: LPI4W, P2625, RPL33A, RPL37A, YPL143W
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein uL29A Chain: h
Molecule details ›
Chain: h
Length: 120 amino acids
Theoretical weight: 13.94 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX84 (Residues: 1-120; Coverage: 100%)
Gene names: D1249, RPL35A, SOS1, YDL191W
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL36A Chain: i
Molecule details ›
Chain: i
Length: 100 amino acids
Theoretical weight: 11.15 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05745 (Residues: 1-100; Coverage: 100%)
Gene names: RPL36A, RPL39A, YM9646.06, YMR194W
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37A Chain: j
Molecule details ›
Chain: j
Length: 88 amino acids
Theoretical weight: 9.88 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P49166 (Residues: 1-88; Coverage: 100%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Sequence domains: Ribosomal protein L37e
60S ribosome subunit biogenesis protein NIP7 Chain: l
Molecule details ›
Chain: l
Length: 181 amino acids
Theoretical weight: 20.41 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q08962 (Residues: 1-181; Coverage: 100%)
Gene names: NIP7, YPL211W
Sequence domains:
Ribosome biogenesis protein ERB1 Chain: m
Molecule details ›
Chain: m
Length: 807 amino acids
Theoretical weight: 91.83 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q04660 (Residues: 1-807; Coverage: 100%)
Gene names: ERB1, YM9796.02C, YMR049C
Sequence domains:
Pescadillo homolog Chain: n
Molecule details ›
Chain: n
Length: 605 amino acids
Theoretical weight: 69.98 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P53261 (Residues: 1-605; Coverage: 100%)
Gene names: NOP7, RRP13, YGR103W, YPH1
Sequence domains:
Ribosome biogenesis protein 15 Chain: o
Molecule details ›
Chain: o
Length: 220 amino acids
Theoretical weight: 25.5 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P53927 (Residues: 1-220; Coverage: 100%)
Gene names: N1954, NOP15, YNL110C
Sequence domains: RNA recognition motif
25S rRNA (cytosine(2870)-C(5))-methyltransferase Chain: q
Molecule details ›
Chain: q
Length: 618 amino acids
Theoretical weight: 69.91 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P40991 (Residues: 1-618; Coverage: 100%)
Gene names: N2428, NOP2, YNA1, YNL061W, YNL2428W
Sequence domains: 16S rRNA methyltransferase RsmB/F
Ribosome biogenesis protein NSA2 Chain: r
Molecule details ›
Chain: r
Length: 261 amino acids
Theoretical weight: 29.79 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P40078 (Residues: 1-261; Coverage: 100%)
Gene names: NSA2, SYGP-ORF47, YER126C
Sequence domains: Ribosomal protein S8e
Ribosome biogenesis protein RLP7 Chain: t
Molecule details ›
Chain: t
Length: 322 amino acids
Theoretical weight: 36.62 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P40693 (Residues: 1-322; Coverage: 100%)
Gene names: N2014, RLP7, RPL7, YNL002C
Sequence domains: Ribosomal protein L30p/L7e
Ribosome biogenesis protein RLP24 Chain: u
Molecule details ›
Chain: u
Length: 199 amino acids
Theoretical weight: 24.03 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q07915 (Residues: 1-199; Coverage: 100%)
Gene names: RLP24, YLR009W
Sequence domains: Ribosomal protein L24e
Nucleolar protein 16 Chain: v
Molecule details ›
Chain: v
Length: 231 amino acids
Theoretical weight: 26.95 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P40007 (Residues: 1-231; Coverage: 100%)
Gene names: NOP16, YER002W
Sequence domains: Ribosome biogenesis protein Nop16
Ribosomal RNA-processing protein 1 Chain: w
Molecule details ›
Chain: w
Length: 278 amino acids
Theoretical weight: 33.25 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P35178 (Residues: 1-278; Coverage: 100%)
Gene names: D4478, RRP1, YDR087C
Sequence domains: Nucleolar protein,Nop52
Ribosome production factor 1 Chain: x
Molecule details ›
Chain: x
Length: 295 amino acids
Theoretical weight: 35.18 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P38805 (Residues: 1-295; Coverage: 100%)
Gene names: RPF1, YHR088W
Sequence domains: Brix domain
Eukaryotic translation initiation factor 6 Chain: y
Molecule details ›
Chain: y
Length: 245 amino acids
Theoretical weight: 26.48 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q12522 (Residues: 1-245; Coverage: 100%)
Gene names: CDC95, LPZ15C, TIF6, YPR016C
Sequence domains: eIF-6 family
Saccharomyces cerevisiae S288C 25S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 3396 nucleotides
Theoretical weight: 1097.49 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
Saccharomyces cerevisiae S288C 5.8S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 158 nucleotides
Theoretical weight: 50.68 KDa
Sequence domains: 5.8S ribosomal RNA
Saccharomyces cerevisiae ITS-2 Chain: 6
Molecule details ›
Chain: 6
Length: 232 nucleotides
Theoretical weight: 74.31 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 2.53Å
Relevant EMDB volumes: EMD-43017

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