› 6cb1

Electron Microscopy
4.6Å resolution

Yeast nucleolar pre-60S ribosomal subunit (state 3)

Released:
DOI: 10.2210/pdb6cb1/pdb
PDB entry 6cb1 coloured by chain, front view.
PDB entry 6cb1 coloured by chain, side view.
PDB entry 6cb1 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae BY4741
Primary publication:
Modular assembly of the nucleolar pre-60S ribosomal subunit.
Sanghai ZA, Miller L, Molloy KR, Barandun J, Hunziker M, Chaker-Margot M, Wang J, Chait BT, Klinge S
Nature 556 126-129 (2018)
PMID: 29512650
Related structures: EMD-7445

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 40-mer (preferred)
PDBe Complex ID:
PDB-CPX-229835 (preferred)
Entry contents:
37 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (40 distinct):
Ribosome biogenesis protein NSA1 Chain: A
Molecule details ›
Chain: A
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
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:
Protein MAK16 Chain: D
Molecule details ›
Chain: D
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 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
Ribosome production factor 1 Chain: I
Molecule details ›
Chain: I
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
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
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
Large ribosomal subunit protein uL23 Chain: X
Molecule details ›
Chain: X
Length: 142 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P04456 (Residues: 1-142; Coverage: 100%)
Gene names: RPL25, YOL127W
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:
Large ribosomal subunit protein eL27A Chain: Z
Molecule details ›
Chain: Z
Length: 136 amino acids
Theoretical weight: 15.57 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0C2H6 (Residues: 1-136; Coverage: 100%)
Gene names: RPL27, RPL27A, YHR010W
Sequence domains: Ribosomal L27e protein family
Nucleolar protein 16 Chain: 7
Molecule details ›
Chain: 7
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
Ribosome biogenesis protein BRX1 Chain: b
Molecule details ›
Chain: b
Length: 291 amino acids
Theoretical weight: 33.08 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 eL30 Chain: c
Molecule details ›
Chain: c
Length: 105 amino acids
Theoretical weight: 11.43 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P14120 (Residues: 1-105; Coverage: 100%)
Gene names: RPL30, RPL32, YGL030W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ribosome biogenesis protein YTM1 Chain: d
Molecule details ›
Chain: d
Length: 465 amino acids
Theoretical weight: 39.59 KDa
Source organism: Saccharomyces cerevisiae BY4741
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 eL34A Chain: g
Molecule details ›
Chain: g
Length: 121 amino acids
Theoretical weight: 13.67 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P87262 (Residues: 1-121; Coverage: 100%)
Gene names: RPL34A, YER056BC, YER056C-A
Sequence domains: Ribosomal protein L34e
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
Large ribosomal subunit protein eL38 Chain: k
Molecule details ›
Chain: k
Length: 78 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P49167 (Residues: 1-78; Coverage: 100%)
Gene names: L8543.2, RPL38, YLR325C
Sequence domains: Ribosomal L38e protein family
rRNA-processing protein EBP2 Chain: m
Molecule details ›
Chain: m
Length: 102 amino acids
Theoretical weight: 8.7 KDa
Source organism: Saccharomyces cerevisiae BY4741
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
ATP-dependent RNA helicase HAS1 Chain: p
Molecule details ›
Chain: p
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:
Ribosome biogenesis protein ERB1 Chain: s
Molecule details ›
Chain: s
Length: 569 amino acids
Theoretical weight: 62.86 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q04660 (Residues: 239-807; Coverage: 71%)
Gene names: ERB1, YM9796.02C, YMR049C
Sequence domains:
Ribosome biogenesis protein RLP7 Chain: t
Molecule details ›
Chain: t
Length: 322 amino acids
Theoretical weight: 35.21 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
BRX1 associated peptide Chain: x
Molecule details ›
Chain: x
Length: 28 amino acids
Theoretical weight: 2.4 KDa
Source organism: Saccharomyces cerevisiae BY4741
Ribosomal RNA-processing protein 1 Chain: z
Molecule details ›
Chain: z
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
35S pre-ribosomal RNA miscRNA Chain: 1
Molecule details ›
Chain: 1
Length: 3396 nucleotides
Theoretical weight: 1097.48 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5.8S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 158 nucleotides
Theoretical weight: 50.68 KDa
Sequence domains: 5.8S ribosomal RNA
ITS2 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: 4.6Å
Relevant EMDB volumes: EMD-7445

Quick links

Citations

17 review citations

Ribosome assembly coming into focus.
Klinge et al. (2019)
16 more

6 mentions without citation

Modular assembly of the nucleolar pre-60S ribosomal subunit.
Sanghai et al. (2018)
5 more