› 6em3

Electron Microscopy
3.2Å resolution

State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes

Released:
DOI: 10.2210/pdb6em3/pdb
PDB entry 6em3 coloured by chain, front view.
PDB entry 6em3 coloured by chain, side view.
PDB entry 6em3 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
Kater L, Thoms M, Barrio-Garcia C, Cheng J, Ismail S, Ahmed YL, Bange G, Kressler D, Berninghausen O, Sinning I, Hurt E, Beckmann R
Cell 171 1599-1610.e14 (2017)
PMID: 29245012
Related structures: EMD-3888

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 33-mer (preferred)
PDBe Complex ID:
PDB-CPX-126971 (preferred)
Entry contents:
30 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (33 distinct):
Ribosome production factor 1 Chain: x
Molecule details ›
Chain: x
Length: 295 amino acids
Theoretical weight: 35.18 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38805 (Residues: 1-295; Coverage: 100%)
Gene names: RPF1, YHR088W
Sequence domains: Brix domain
Large ribosomal subunit protein uL30A Chain: F
Molecule details ›
Chain: F
Length: 244 amino acids
Theoretical weight: 27.69 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05737 (Residues: 1-244; Coverage: 100%)
Gene names: RPL6A, RPL7A, RPL8A, YGL076C, YL8A
Sequence domains:
Protein MAK16 Chain: 3
Molecule details ›
Chain: 3
Length: 306 amino acids
Theoretical weight: 35.75 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P10962 (Residues: 1-306; Coverage: 100%)
Gene names: MAK16, YAL025C
Sequence domains:
Ribosomal RNA-processing protein 1 Chain: 4
Molecule details ›
Chain: 4
Length: 278 amino acids
Theoretical weight: 33.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P35178 (Residues: 1-278; Coverage: 100%)
Gene names: D4478, RRP1, YDR087C
Sequence domains: Nucleolar protein,Nop52
Ribosome biogenesis protein NSA1 Chain: 5
Molecule details ›
Chain: 5
Length: 463 amino acids
Theoretical weight: 51.98 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53136 (Residues: 1-463; Coverage: 100%)
Gene names: G2990, NSA1, YGL111W
Ribosome biogenesis protein BRX1 Chain: A
Molecule details ›
Chain: A
Length: 291 amino acids
Theoretical weight: 33.59 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08235 (Residues: 1-291; Coverage: 100%)
Gene names: BRX1, YOL077C
Sequence domains: Brix domain
rRNA-processing protein EBP2 Chain: J
Molecule details ›
Chain: J
Length: 427 amino acids
Theoretical weight: 49.84 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P36049 (Residues: 1-427; Coverage: 100%)
Gene names: EBP2, YKL172W, YKL636
Sequence domains: Eukaryotic rRNA processing protein EBP2
Nucleolar protein 16 Chain: v
Molecule details ›
Chain: v
Length: 231 amino acids
Theoretical weight: 26.95 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40007 (Residues: 1-231; Coverage: 100%)
Gene names: NOP16, YER002W
Sequence domains: Ribosome biogenesis protein Nop16
Large ribosomal subunit protein uL4A Chain: C
Molecule details ›
Chain: C
Length: 362 amino acids
Theoretical weight: 39.16 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P10664 (Residues: 1-362; Coverage: 100%)
Gene names: RPL2, RPL2A, RPL4A, YBR0315, YBR031W
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 S288C
UniProt:
  • Canonical: P38061 (Residues: 1-130; Coverage: 100%)
Gene names: RPL32, YBL0838, YBL092W
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL6A Chain: E
Molecule details ›
Chain: E
Length: 176 amino acids
Theoretical weight: 20 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02326 (Residues: 1-176; Coverage: 100%)
Gene names: RPL17A, RPL6A, YL16A, YML073C
Sequence domains: Ribosomal protein L6e
Large ribosomal subunit protein eL33A Chain: f
Molecule details ›
Chain: f
Length: 107 amino acids
Theoretical weight: 12.18 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05744 (Residues: 1-107; Coverage: 100%)
Gene names: LPI4W, P2625, RPL33A, RPL37A, YPL143W
Sequence domains: Ribosomal protein L35Ae
Structure domains: translation elongation factor selb, chain A, domain 4
Large ribosomal subunit protein eL8A Chain: G
Molecule details ›
Chain: G
Length: 256 amino acids
Theoretical weight: 28.18 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P17076 (Residues: 1-256; Coverage: 100%)
Gene names: MAK7, RPL4A, RPL8A, YHL033C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Structure domains: 60s Ribosomal Protein L30; Chain: A;
Large ribosomal subunit protein uL29A Chain: h
Molecule details ›
Chain: h
Length: 120 amino acids
Theoretical weight: 13.94 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX84 (Residues: 1-120; Coverage: 100%)
Gene names: D1249, RPL35A, SOS1, YDL191W
Sequence domains: Ribosomal L29 protein
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Large ribosomal subunit protein eL36B Chain: i
Molecule details ›
Chain: i
Length: 100 amino acids
Theoretical weight: 11.16 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: O14455 (Residues: 1-100; Coverage: 100%)
Gene names: RPL36B, RPL39B, YPL249BC, YPL249C-A
Sequence domains: Ribosomal protein L36e
Structure domains: 60S ribosomal protein L36
Large ribosomal subunit protein eL37A Chain: j
Molecule details ›
Chain: j
Length: 88 amino acids
Theoretical weight: 9.88 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P49166 (Residues: 1-88; Coverage: 100%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL13A Chain: L
Molecule details ›
Chain: L
Length: 199 amino acids
Theoretical weight: 22.6 KDa
Source organism: Saccharomyces cerevisiae S288C
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 S288C
UniProt:
  • Canonical: P36105 (Residues: 1-138; Coverage: 100%)
Gene names: RPL14A, YKL006W, YKL153
Sequence domains:
Structure domains: SH3 type barrels.
Large ribosomal subunit protein eL15A Chain: N
Molecule details ›
Chain: N
Length: 204 amino acids
Theoretical weight: 24.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05748 (Residues: 1-204; Coverage: 100%)
Gene names: RPL10A, RPL13A, RPL15A, YL10A, YLR029C
Sequence domains: Ribosomal L15
Structure domains: Ribosomal protein l15e
Large ribosomal subunit protein uL13A Chain: O
Molecule details ›
Chain: O
Length: 199 amino acids
Theoretical weight: 22.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P26784 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13, RPL16A, RPL21A, YIL133C
Sequence domains: Ribosomal protein L13
Structure domains:
Large ribosomal subunit protein uL22A Chain: P
Molecule details ›
Chain: P
Length: 184 amino acids
Theoretical weight: 20.59 KDa
Source organism: Saccharomyces cerevisiae S288C
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 S288C
UniProt:
  • Canonical: P0CX49 (Residues: 1-186; Coverage: 100%)
Gene names: RP28A, RPL18A, YOL120C
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Structure domains: Ribosomal Protein L15; Chain: K; domain 2
Large ribosomal subunit protein eL20A Chain: S
Molecule details ›
Chain: S
Length: 172 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae S288C
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
Structure domains: Ubiquitin-like (UB roll)
Large ribosomal subunit protein uL24A Chain: Y
Molecule details ›
Chain: Y
Length: 127 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05743 (Residues: 1-127; Coverage: 100%)
Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:
Structure domains: SH3 type barrels.
ATP-dependent RNA helicase HAS1 Chain: D
Molecule details ›
Chain: D
Length: 505 amino acids
Theoretical weight: 56.8 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03532 (Residues: 1-505; Coverage: 100%)
Gene names: HAS1, YMR290C
Sequence domains:
Proteasome-interacting protein CIC1 Chain: K
Molecule details ›
Chain: K
Length: 376 amino acids
Theoretical weight: 42.6 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38779 (Residues: 1-376; Coverage: 100%)
Gene names: CIC1, NSA3, YHR052W
Sequence domains: Ribosomal protein L1p/L10e family
Pescadillo homolog Chain: n
Molecule details ›
Chain: n
Length: 605 amino acids
Theoretical weight: 69.98 KDa
Source organism: Saccharomyces cerevisiae S288C
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 S288C
UniProt:
  • Canonical: P53927 (Residues: 1-220; Coverage: 100%)
Gene names: N1954, NOP15, YNL110C
Sequence domains: RNA recognition motif
Ribosome biogenesis protein RLP7 Chain: t
Molecule details ›
Chain: t
Length: 322 amino acids
Theoretical weight: 36.62 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40693 (Residues: 1-322; Coverage: 100%)
Gene names: N2014, RLP7, RPL7, YNL002C
Sequence domains: Ribosomal protein L30p/L7e
Ribosome biogenesis protein ERB1 Chain: B
Molecule details ›
Chain: B
Length: 807 amino acids
Theoretical weight: 91.83 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q04660 (Residues: 1-807; Coverage: 100%)
Gene names: ERB1, YM9796.02C, YMR049C
Sequence domains:
25S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 3396 nucleotides
Theoretical weight: 1097.49 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
5.8S ribosomal RNA Chain: 6
Molecule details ›
Chain: 6
Length: 232 nucleotides
Theoretical weight: 74.31 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-3888

Quick links

Citations

14 review citations

Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors.
Sáez-Vásquez et al. (2019)
13 more

10 mentions without citation

RNA folding and functions of RNA helicases in ribosome biogenesis.
Mitterer et al. (2022)
9 more