6ft6

Electron Microscopy
3.9Å resolution

Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors

Released:
Related structures: EMD-4302

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
Entry contents:
54 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (57 distinct):
60S ribosomal protein L2-A Chain: A
Molecule details ›
Chain: A
Length: 254 amino acids
Theoretical weight: 27.46 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX45 (Residues: 1-254; Coverage: 100%)
Gene names: RPL2A, RPL5B, YFR031BC, YFR031C-A
Sequence domains:
60S ribosomal protein L3 Chain: B
Molecule details ›
Chain: B
Length: 387 amino acids
Theoretical weight: 43.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P14126 (Residues: 1-387; Coverage: 100%)
Gene names: MAK8, RPL3, TCM1, YOR063W, YOR29-14
Sequence domains: Ribosomal protein L3
60S ribosomal protein L4-A 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:
60S ribosomal protein L5 Chain: D
Molecule details ›
Chain: D
Length: 297 amino acids
Theoretical weight: 33.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P26321 (Residues: 1-297; Coverage: 100%)
Gene names: LPI14W, RPL1, RPL1A, RPL5, YPL131W
Sequence domains:
60S ribosomal protein L6-A 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
60S ribosomal protein L7-A 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:
60S ribosomal protein L8-A 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
60S ribosomal protein L9-A Chain: H
Molecule details ›
Chain: H
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05738 (Residues: 1-191; Coverage: 100%)
Gene names: RPL8A, RPL9, RPL9A, YGL147C
Sequence domains: Ribosomal protein L6
Bud site selection protein 20 Chain: I
Molecule details ›
Chain: I
Length: 166 amino acids
Theoretical weight: 18.55 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08004 (Residues: 1-166; Coverage: 100%)
Gene names: BUD20, YLR074C
Sequence domains: Zinc-finger double-stranded RNA-binding
60S ribosomal protein L11-A Chain: J
Molecule details ›
Chain: J
Length: 174 amino acids
Theoretical weight: 19.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C0W9 (Residues: 1-174; Coverage: 100%)
Gene names: P8283.14, RP39A, RPL11A, RPL16A, YPR102C
Sequence domains:
60S ribosomal protein L13-A 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
60S ribosomal protein L14-A 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: Ribosomal protein L14
60S ribosomal protein L15-A 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
60S ribosomal protein L16-A 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
60S ribosomal protein L17-A 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
60S ribosomal protein L18-A 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
60S ribosomal protein L19-A Chain: R
Molecule details ›
Chain: R
Length: 189 amino acids
Theoretical weight: 21.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX82 (Residues: 1-189; Coverage: 100%)
Gene names: RPL19A, RPL23A, YBR084BC, YBR084C-A, YL14A
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L20-A 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
60S ribosomal protein L21-A Chain: T
Molecule details ›
Chain: T
Length: 160 amino acids
Theoretical weight: 18.28 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02753 (Residues: 1-160; Coverage: 100%)
Gene names: RPL21A, URP1, YBR1401, YBR191W
Sequence domains: Ribosomal protein L21e
60S ribosomal protein L22-A Chain: U
Molecule details ›
Chain: U
Length: 121 amino acids
Theoretical weight: 13.71 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05749 (Residues: 1-121; Coverage: 100%)
Gene names: L2168, RPL22A, YLR061W
Sequence domains: Ribosomal L22e protein family
60S ribosomal protein L23-A Chain: V
Molecule details ›
Chain: V
Length: 137 amino acids
Theoretical weight: 14.49 KDa
Source organism: Saccharomyces cerevisiae S288C
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 S288C
UniProt:
  • Canonical: P33201 (Residues: 1-236; Coverage: 100%)
Gene names: MRT4, YKL009W, YKL160
Sequence domains:
60S ribosomal protein L25 Chain: X
Molecule details ›
Chain: X
Length: 142 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04456 (Residues: 1-142; Coverage: 100%)
Gene names: RPL25, YOL127W
Sequence domains:
60S ribosomal protein L26-A 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:
60S ribosomal protein L27-A Chain: Z
Molecule details ›
Chain: Z
Length: 136 amino acids
Theoretical weight: 15.57 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C2H6 (Residues: 1-136; Coverage: 100%)
Gene names: RPL27, RPL27A, YHR010W
Sequence domains: Ribosomal L27e protein family
60S ribosomal protein L28 Chain: a
Molecule details ›
Chain: a
Length: 149 amino acids
Theoretical weight: 16.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P02406 (Residues: 1-149; Coverage: 100%)
Gene names: CYH2, RPL28, YGL103W
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Nucleolar GTP-binding protein 1 Chain: b
Molecule details ›
Chain: b
Length: 647 amino acids
Theoretical weight: 74.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02892 (Residues: 1-647; Coverage: 100%)
Gene names: LPG15W, NOG1, YPL093W
Sequence domains:
60S ribosomal protein L30 Chain: c
Molecule details ›
Chain: c
Length: 105 amino acids
Theoretical weight: 11.43 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P14120 (Residues: 1-105; Coverage: 100%)
Gene names: RPL30, RPL32, YGL030W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L31-A Chain: d
Molecule details ›
Chain: d
Length: 113 amino acids
Theoretical weight: 12.98 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C2H8 (Residues: 1-113; Coverage: 100%)
Gene names: D2478, RPL31A, RPL34, RPL34A, YDL075W
Sequence domains: Ribosomal protein L31e
60S ribosomal protein L32 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
60S ribosomal protein L33-A 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
60S ribosomal protein L34-A Chain: g
Molecule details ›
Chain: g
Length: 121 amino acids
Theoretical weight: 13.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P87262 (Residues: 1-121; Coverage: 100%)
Gene names: RPL34A, YER056BC, YER056C-A
Sequence domains: Ribosomal protein L34e
60S ribosomal protein L35-A 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
60S ribosomal protein L36-A Chain: i
Molecule details ›
Chain: i
Length: 100 amino acids
Theoretical weight: 11.15 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05745 (Residues: 1-100; Coverage: 100%)
Gene names: RPL36A, RPL39A, YM9646.06, YMR194W
Sequence domains: Ribosomal protein L36e
60S ribosomal protein L37-A 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
60S ribosomal protein L38 Chain: k
Molecule details ›
Chain: k
Length: 78 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P49167 (Residues: 1-78; Coverage: 100%)
Gene names: L8543.2, RPL38, YLR325C
Sequence domains: Ribosomal L38e protein family
60S ribosomal protein L39 Chain: l
Molecule details ›
Chain: l
Length: 51 amino acids
Theoretical weight: 6.36 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04650 (Residues: 1-51; Coverage: 100%)
Gene names: J0360, RPL39, RPL46, SPB2, YJL189W
Sequence domains: Ribosomal L39 protein
Nucleolar GTP-binding protein 2 Chain: m
Molecule details ›
Chain: m
Length: 486 amino acids
Theoretical weight: 55.59 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53742 (Residues: 1-486; Coverage: 100%)
Gene names: N3484, NOG2, YNR053C
Sequence domains:
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:
60S ribosomal protein L43-A Chain: p
Molecule details ›
Chain: p
Length: 92 amino acids
Theoretical weight: 10.11 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX25 (Residues: 1-92; Coverage: 100%)
Gene names: RPL43A, YP9499.02, YPR043W
Sequence domains: Ribosomal L37ae protein family
Ribosome biogenesis protein NSA2 Chain: r
Molecule details ›
Chain: r
Length: 261 amino acids
Theoretical weight: 29.79 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40078 (Residues: 1-261; Coverage: 100%)
Gene names: NSA2, SYGP-ORF47, YER126C
Sequence domains: Ribosomal protein S8e
Nuclear GTP-binding protein NUG1 Chain: s
Molecule details ›
Chain: s
Length: 520 amino acids
Theoretical weight: 57.8 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40010 (Residues: 1-520; Coverage: 100%)
Gene names: NUG1, YER006W
Sequence domains:
Ribosome biogenesis protein RLP24 Chain: u
Molecule details ›
Chain: u
Length: 199 amino acids
Theoretical weight: 24.03 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q07915 (Residues: 1-199; Coverage: 100%)
Gene names: RLP24, YLR009W
Sequence domains: Ribosomal protein L24e
Ribosome biogenesis protein RPF2 Chain: v
Molecule details ›
Chain: v
Length: 344 amino acids
Theoretical weight: 39.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P36160 (Residues: 1-344; Coverage: 100%)
Gene names: RPF2, YKR081C, YKR401
Sequence domains: Brix domain
Regulator of ribosome biosynthesis Chain: w
Molecule details ›
Chain: w
Length: 203 amino acids
Theoretical weight: 23 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08746 (Residues: 1-203; Coverage: 100%)
Gene names: RRS1, YOR294W
Sequence domains: Ribosome biogenesis regulatory protein (RRS1)
Ribosome assembly protein 4 Chain: x
Molecule details ›
Chain: x
Length: 515 amino acids
Theoretical weight: 57.11 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25382 (Residues: 1-515; Coverage: 100%)
Gene names: RSA4, YCR072C, YCR72C
Sequence domains:
Eukaryotic translation initiation factor 6 Chain: y
Molecule details ›
Chain: y
Length: 245 amino acids
Theoretical weight: 26.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12522 (Residues: 1-245; Coverage: 100%)
Gene names: CDC95, LPZ15C, TIF6, YPR016C
Sequence domains: eIF-6 family
UPF0642 protein YBL028C Chain: z
Molecule details ›
Chain: z
Length: 106 amino acids
Theoretical weight: 12.44 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38202 (Residues: 1-106; Coverage: 100%)
Gene names: YBL028C, YBL0423
Sequence domains: Protein of unknown function (DUF2423)
Probable metalloprotease ARX1 Chain: 4
Molecule details ›
Chain: 4
Length: 593 amino acids
Theoretical weight: 65.29 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03862 (Residues: 1-593; Coverage: 100%)
Gene names: ARX1, YD8557.10c, YDR101C
Sequence domains: Metallopeptidase family M24
rRNA-processing protein CGR1 Chain: 5
Molecule details ›
Chain: 5
Length: 120 amino acids
Theoretical weight: 14.46 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53188 (Residues: 1-120; Coverage: 100%)
Gene names: CGR1, YGL029W
Sequence domains: Cgr1 family
Exosome complex exonuclease RRP6 Chain: KK
Molecule details ›
Chain: KK
Length: 733 amino acids
Theoretical weight: 84.16 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12149 (Residues: 1-733; Coverage: 100%)
Gene names: RRP6, UNC733, YOR001W
Sequence domains:
Exosome complex protein LRP1 Chain: LL
Molecule details ›
Chain: LL
Length: 184 amino acids
Theoretical weight: 21.09 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P38801 (Residues: 1-184; Coverage: 100%)
Gene names: LRP1, RRP47, YC1D, YHR081W
Sequence domains: Sas10/Utp3/C1D family
ATP-dependent RNA helicase DOB1 Chain: MM
Molecule details ›
Chain: MM
Length: 1011 amino acids
Theoretical weight: 115.23 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P47047 (Residues: 80-1073; Coverage: 93%)
Gene names: DOB1, J1158, MTR4, YJL050W
Sequence domains:
MPP6 Chain: NN
Molecule details ›
Chain: NN
Length: 11 amino acids
Theoretical weight: 954 Da
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
7S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 162 nucleotides
Theoretical weight: 52 KDa
Sequence domains: 5.8S ribosomal RNA
25S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 3396 nucleotides
Theoretical weight: 1097.49 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: 3
Molecule details ›
Chain: 3
Length: 121 nucleotides
Theoretical weight: 38.95 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-4302
Expression system: Escherichia coli