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- EMDB-4302: Structure of the Nop53 pre-60S particle bound to the exosome nucl... -

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Entry
Database: EMDB / ID: 4302
TitleStructure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors
Map dataStructure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors
SampleStructure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors
  • pre-60S particle
  • exosome nuclear cofactors
  • (nucleic-acidNucleic acid) x 3
  • (60S ribosomal protein ...) x 35
  • Bud site selection protein 20
  • (Ribosome assembly ...) x 2
  • (Nucleolar GTP-binding protein ...) x 2
  • Pescadillo homolog
  • (Ribosome biogenesis protein ...) x 3
  • Nuclear GTP-binding protein NUG1
  • Regulator of ribosome biosynthesis
  • Eukaryotic translation initiation factor 6
  • UPF0642 protein YBL028C
  • Probable metalloprotease ARX1
  • rRNA-processing protein CGR1
  • (Exosome complex ...) x 2
  • ATP-dependent RNA helicase DOB1
  • MPP6
  • (ligand) x 3
Function / homologyRibosomal protein L31e domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein L39e domain superfamily / Zinc-finger double-stranded RNA-binding / Ribosomal protein L4 domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13, conserved site / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L5 domain superfamily ...Ribosomal protein L31e domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein L39e domain superfamily / Zinc-finger double-stranded RNA-binding / Ribosomal protein L4 domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13, conserved site / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L5 domain superfamily / Ribosomal protein L15e core domain superfamily / Zinc finger, double-stranded RNA binding / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L18e, conserved site / Ribosomal protein L19/L19e conserved site / Nucleolar GTP-binding protein 1 / Ribosomal protein L5, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L29/L35 superfamily / Creatinase/aminopeptidase-like / Ribosomal protein L19/L19e superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosome assembly factor Mrt4 / Ribosomal protein L5, N-terminal / OBG-type guanine nucleotide-binding (G) domain / Nucleolar GTP-binding protein 2 / Ribosomal protein L15 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / 50S ribosomal protein L30e-like / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / P-loop containing nucleoside triphosphate hydrolase / 60S ribosomal protein L4, C-terminal domain / rRNA-processing arch domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L18e/L15P / Ribosomal protein L15e, conserved site / Zinc finger C2H2 superfamily / Ribosomal protein L25/L23 / Ribosomal protein L19/L19e, domain 1 / WD40/YVTN repeat-like-containing domain superfamily / Guanine nucleotide-binding protein-like 3, N-terminal domain / Ribosomal protein L2, domain 3 / Ribosomal protein L2, domain 2 / Helicase superfamily 1/2, ATP-binding domain / Zinc finger C2H2-type / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / ATP-dependent RNA helicase Ski2-like / Ribosomal protein L30, N-terminal / NOG, C-terminal / NLE / Nucleolar GTP-binding protein 2, N-terminal domain / ATP-dependent RNA helicase Ski2, C-terminal / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain / WD40-repeat-containing domain / G-protein beta WD-40 repeat / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L14P, conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Uncharacterised protein family UPF0642 / Ribosomal protein L37e, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L34e, conserved site / Ribosomal L18e/L15P superfamily / WD40-repeat-containing domain superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein L35Ae / Ribosomal L22e protein family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L32 / 3'-5' exonuclease / Ribosomal protein L13e / Ribosomal protein L19e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L24e / Ribosomal L37ae protein family / Ribosomal protein S8e / Ribosomal protein L34e / Ribosomal protein L31e / Ribosomal protein L6e / Ribosomal protein L36e / Ribosomal protein L21e / Ribosomal L39 protein
Function and homology information
SourceSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsSchuller JM / Falk S / Conti E
CitationJournal: Science / Year: 2018
Title: Structure of the nuclear exosome captured on a maturing preribosome.
Authors: Jan Michael Schuller / Sebastian Falk / Lisa Fromm / Ed Hurt / Elena Conti
Abstract: The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex ...The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60) during 7-to-5.8 rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 particle, which harbors the 5.8 rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 rRNA, captures the 3' extension of the 5.8 rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 substrate to process rRNA during ribosome maturation.
Validation ReportPDB-ID: 6ft6

SummaryFull reportAbout validation report
DateDeposition: Feb 20, 2018 / Header (metadata) release: Mar 28, 2018 / Map release: Mar 28, 2018 / Last update: Aug 29, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ft6
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4302.map.gz (map file in CCP4 format, 340737 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
440 pix
1.35 Å/pix.
= 594. Å
440 pix
1.35 Å/pix.
= 594. Å
440 pix
1.35 Å/pix.
= 594. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.013 (by author), 0.013 (movie #1):
Minimum - Maximum-0.024440063 - 0.071778
Average (Standard dev.)0.00014779603 (0.0032518958)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions440440440
Origin0.0.0.
Limit439.439.439.
Spacing440440440
CellA=B=C: 594.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z594.000594.000594.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0240.0720.000

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Supplemental data

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Sample components

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Entire Structure of the Nop53 pre-60S particle bound to the exosome nucl...

EntireName: Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors
Number of components: 63

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Component #1: protein, Structure of the Nop53 pre-60S particle bound to the exo...

ProteinName: Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors
Recombinant expression: No

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Component #2: protein, pre-60S particle

ProteinName: pre-60S particle / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #3: protein, exosome nuclear cofactors

ProteinName: exosome nuclear cofactors / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: nucleic-acid, 7S ribosomal RNA

Nucleic-acidName: 7S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAACUUUCAA CAACGGAUCU CUUGGUUCUC GCAUCGAUGA AGAACGCAGC GAAAUGCGAU ACGUAAUGUG AAUUGCAGAA UUCCGUGAAU CAUCGAAUCU UUGAACGCAC AUUGCGCCCC UUGGUAUUCC AGGGGGCAUG CCUGUUUGAG CGUCAUAAAA UU
MassTheoretical: 51.999754 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #5: protein, 60S ribosomal protein L2-A

ProteinName: 60S ribosomal protein L2-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.463574 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #6: protein, 60S ribosomal protein L3

ProteinName: 60S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.850793 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #7: protein, 60S ribosomal protein L4-A

ProteinName: 60S ribosomal protein L4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.159125 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #8: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.764828 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #9: protein, 60S ribosomal protein L6-A

ProteinName: 60S ribosomal protein L6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.000564 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #10: protein, 60S ribosomal protein L7-A

ProteinName: 60S ribosomal protein L7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.686281 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: protein, 60S ribosomal protein L8-A

ProteinName: 60S ribosomal protein L8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.17582 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #12: protein, 60S ribosomal protein L9-A

ProteinName: 60S ribosomal protein L9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.605061 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #13: protein, Bud site selection protein 20

ProteinName: Bud site selection protein 20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.546982 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #14: protein, 60S ribosomal protein L11-A

ProteinName: 60S ribosomal protein L11-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.755691 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #15: protein, 60S ribosomal protein L13-A

ProteinName: 60S ribosomal protein L13-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.604164 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #16: protein, 60S ribosomal protein L14-A

ProteinName: 60S ribosomal protein L14-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.195066 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, 60S ribosomal protein L15-A

ProteinName: 60S ribosomal protein L15-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.482357 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: protein, 60S ribosomal protein L16-A

ProteinName: 60S ribosomal protein L16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.247227 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #19: protein, 60S ribosomal protein L17-A

ProteinName: 60S ribosomal protein L17-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.589518 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #20: protein, 60S ribosomal protein L18-A

ProteinName: 60S ribosomal protein L18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.609252 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #21: protein, 60S ribosomal protein L19-A

ProteinName: 60S ribosomal protein L19-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.762316 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #22: protein, 60S ribosomal protein L20-A

ProteinName: 60S ribosomal protein L20-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.478852 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #23: protein, 60S ribosomal protein L21-A

ProteinName: 60S ribosomal protein L21-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.279266 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #24: protein, 60S ribosomal protein L22-A

ProteinName: 60S ribosomal protein L22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.711359 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #25: protein, 60S ribosomal protein L23-A

ProteinName: 60S ribosomal protein L23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.49395 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #26: protein, Ribosome assembly factor MRT4

ProteinName: Ribosome assembly factor MRT4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.098012 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #27: protein, 60S ribosomal protein L25

ProteinName: 60S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.787612 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #28: protein, 60S ribosomal protein L26-A

ProteinName: 60S ribosomal protein L26-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.265784 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #29: protein, 60S ribosomal protein L27-A

ProteinName: 60S ribosomal protein L27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.56836 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #30: protein, 60S ribosomal protein L28

ProteinName: 60S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.761666 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #31: protein, Nucleolar GTP-binding protein 1

ProteinName: Nucleolar GTP-binding protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.531227 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #32: protein, 60S ribosomal protein L30

ProteinName: 60S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.430364 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #33: protein, 60S ribosomal protein L31-A

ProteinName: 60S ribosomal protein L31-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.980158 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #34: protein, 60S ribosomal protein L32

ProteinName: 60S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.809441 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #35: protein, 60S ribosomal protein L33-A

ProteinName: 60S ribosomal protein L33-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.17713 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #36: protein, 60S ribosomal protein L34-A

ProteinName: 60S ribosomal protein L34-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.673196 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #37: protein, 60S ribosomal protein L35-A

ProteinName: 60S ribosomal protein L35-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.94264 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #38: protein, 60S ribosomal protein L36-A

ProteinName: 60S ribosomal protein L36-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.151259 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #39: protein, 60S ribosomal protein L37-A

ProteinName: 60S ribosomal protein L37-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.877395 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #40: protein, 60S ribosomal protein L38

ProteinName: 60S ribosomal protein L38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.845561 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #41: protein, 60S ribosomal protein L39

ProteinName: 60S ribosomal protein L39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.35864 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #42: protein, Nucleolar GTP-binding protein 2

ProteinName: Nucleolar GTP-binding protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.58559 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #43: protein, Pescadillo homolog

ProteinName: Pescadillo homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 69.984148 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #44: protein, 60S ribosomal protein L43-A

ProteinName: 60S ribosomal protein L43-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.112952 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #45: protein, Ribosome biogenesis protein NSA2

ProteinName: Ribosome biogenesis protein NSA2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.786783 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #46: protein, Nuclear GTP-binding protein NUG1

ProteinName: Nuclear GTP-binding protein NUG1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.798652 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #47: protein, Ribosome biogenesis protein RLP24

ProteinName: Ribosome biogenesis protein RLP24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.02765 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #48: protein, Ribosome biogenesis protein RPF2

ProteinName: Ribosome biogenesis protein RPF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.665789 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #49: protein, Regulator of ribosome biosynthesis

ProteinName: Regulator of ribosome biosynthesis / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.00141 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #50: protein, Ribosome assembly protein 4

ProteinName: Ribosome assembly protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.106781 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #51: protein, Eukaryotic translation initiation factor 6

ProteinName: Eukaryotic translation initiation factor 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.476605 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #52: protein, UPF0642 protein YBL028C

ProteinName: UPF0642 protein YBL028C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.435429 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #53: nucleic-acid, 25S ribosomal RNA

Nucleic-acidName: 25S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUUGACCUC AAAUCAGGUA GGAGUACCCG CUGAACUUAA GCAUAUCAAU AAGCGGAGGA AAAGAAACCA ACCGGGAUUG CCUUAGUAAC GGCGAGUGAA GCGGCAAAAG CUCAAAUUUG AAAUCUGGUA CCUUCGGUGC CCGAGUUGUA AUUUGGAGAG GGCAACUUUG GGGCCGUUCC UUGUCUAUGU UCCUUGGAAC AGGACGUCAU AGAGGGUGAG AAUCCCGUGU GGCGAGGAGU GCGGUUCUUU GUAAAGUGCC UUCGAAGAGU CGAGUUGUUU GGGAAUGCAG CUCUAAGUGG GUGGUAAAUU CCAUCUAAAG CUAAAUAUUG GCGAGAGACC GAUAGCGAAC AAGUACAGUG AUGGAAAGAU GAAAAGAACU UUGAAAAGAG AGUGAAAAAG UACGUGAAAU UGUUGAAAGG GAAGGGCAUU UGAUCAGACA UGGUGUUUUG UGCCCUCUGC UCCUUGUGGG UAGGGGAAUC UCGCAUUUCA CUGGGCCAGC AUCAGUUUUG GUGGCAGGAU AAAUCCAUAG GAAUGUAGCU UGCCUCGGUA AGUAUUAUAG CCUGUGGGAA UACUGCCAGC UGGGACUGAG GACUGCGACG UAAGUCAAGG AUGCUGGCAU AAUGGUUAUA UGCCGCCCGU CUUGAAACAC GGACCAAGGA GUCUAACGUC UAUGCGAGUG UUUGGGUGUA AAACCCAUAC GCGUAAUGAA AGUGAACGUA GGUUGGGGCC UCGCAAGAGG UGCACAAUCG ACCGAUCCUG AUGUCUUCGG AUGGAUUUGA GUAAGAGCAU AGCUGUUGGG ACCCGAAAGA UGGUGAACUA UGCCUGAAUA GGGUGAAGCC AGAGGAAACU CUGGUGGAGG CUCGUAGCGG UUCUGACGUG CAAAUCGAUC GUCGAAUUUG GGUAUAGGGG CGAAAGACUA AUCGAACCAU CUAGUAGCUG GUUCCUGCCG AAGUUUCCCU CAGGAUAGCA GAAGCUCGUA UCAGUUUUAU GAGGUAAAGC GAAUGAUUAG AGGUUCCGGG GUCGAAAUGA CCUUGACCUA UUCUCAAACU UUAAAUAUGU AAGAAGUCCU UGUUACUUAA UUGAACGUGG ACAUUUGAAU GAAGAGCUUU UAGUGGGCCA UUUUUGGUAA GCAGAACUGG CGAUGCGGGA UGAACCGAAC GUAGAGUUAA GGUGCCGGAA UACACGCUCA UCAGACACCA CAAAAGGUGU UAGUUCAUCU AGACAGCCGG ACGGUGGCCA UGGAAGUCGG AAUCCGCUAA GGAGUGUGUA ACAACUCACC GGCCGAAUGA ACUAGCCCUG AAAAUGGAUG GCGCUCAAGC GUGUUACCUA UACUCUACCG UCAGGGUUGA UAUGAUGCCC UGACGAGUAG GCAGGCGUGG AGGUCAGUGA CGAAGCCUAG ACCGUAAGGU CGGGUCGAAC GGCCUCUAGU GCAGAUCUUG GUGGUAGUAG CAAAUAUUCA AAUGAGAACU UUGAAGACUG AAGUGGGGAA AGGUUCCACG UCAACAGCAG UUGGACGUGG GUUAGUCGAU CCUAAGAGAU GGGGAAGCUC CGUUUCAAAG GCCUGAUUUU AUGCAGGCCA CCAUCGAAAG GGAAUCCGGU UAAGAUUCCG GAACCUGGAU AUGGAUUCUU CACGGUAACG UAACUGAAUG UGGAGACGUC GGCGCGAGCC CUGGGAGGAG UUAUCUUUUC UUCUUAACAG CUUAUCACCC CGGAAUUGGU UUAUCCGGAG AUGGGGUCUU AUGGCUGGAA GAGGCCAGCA CCUUUGCUGG CUCCGGUGCG CUUGUGACGG CCCGUGAAAA UCCACAGGAA GGAAUAGUUU UCAUGCCAGG UCGUACUGAU AACCGCAGCA GGUCUCCAAG GUGAACAGCC UCUAGUUGAU AGAAUAAUGU AGAUAAGGGA AGUCGGCAAA AUAGAUCCGU AACUUCGGGA UAAGGAUUGG CUCUAAGGGU CGGGUAGUGA GGGCCUUGGU CAGACGCAGC GGGCGUGCUU GUGGACUGCU UGGUGGGGCU UGCUCUGCUA GGCGGACUAC UUGCGUGCCU UGUUGUAGAC GGCCUUGGUA GGUCUCUUGU AGACCGUCGC UUGCUACAAU UAACGAUCAA CUUAGAACUG GUACGGACAA GGGGAAUCUG ACUGUCUAAU UAAAACAUAG CAUUGCGAUG GUCAGAAAGU GAUGUUGACG CAAUGUGAUU UCUGCCCAGU GCUCUGAAUG UCAAAGUGAA GAAAUUCAAC CAAGCGCGGG UAAACGGCGG GAGUAACUAU GACUCUCUUA AGGUAGCCAA AUGCCUCGUC AUCUAAUUAG UGACGCGCAU GAAUGGAUUA ACGAGAUUCC CACUGUCCCU AUCUACUAUC UAGCGAAACC ACAGCCAAGG GAACGGGCUU GGCAGAAUCA GCGGGGAAAG AAGACCCUGU UGAGCUUGAC UCUAGUUUGA CAUUGUGAAG AGACAUAGAG GGUGUAGAAU AAGUGGGAGC UUCGGCGCCA GUGAAAUACC ACUACCUUUA UAGUUUCUUU ACUUAUUCAA UGAAGCGGAG CUGGAAUUCA UUUUCCACGU UCUAGCAUUC AAGGUCCCAU UCGGGGCUGA UCCGGGUUGA AGACAUUGUC AGGUGGGGAG UUUGGCUGGG GCGGCACAUC UGUUAAACGA UAACGCAGAU GUCCUAAGGG GGGCUCAUGG AGAACAGAAA UCUCCAGUAG AACAAAAGGG UAAAAGCCCC CUUGAUUUUG AUUUUCAGUG UGAAUACAAA CCAUGAAAGU GUGGCCUAUC GAUCCUUUAG UCCCUCGGAA UUUGAGGCUA GAGGUGCCAG AAAAGUUACC ACAGGGAUAA CUGGCUUGUG GCAGUCAAGC GUUCAUAGCG ACAUUGCUUU UUGAUUCUUC GAUGUCGGCU CUUCCUAUCA UACCGAAGCA GAAUUCGGUA AGCGUUGGAU UGUUCACCCA CUAAUAGGGA ACGUGAGCUG GGUUUAGACC GUCGUGAGAC AGGUUAGUUU UACCCUACUG AUGAAUGUUA CCGCAAUAGU AAUUGAACUU AGUACGAGAG GAACAGUUCA UUCGGAUAAU UGGUUUUUGC GGCUGUCUGA UCAGGCAUUG CCGCGAAGCU ACCAUCCGCU GGAUUAUGGC UGAACGCCUC UAAGUCAGAA UCCAUGCUAG AACGCGGUGA UUUCUUUGCU CCACACAAUA UAGAUGGAUA CGAAUAAGGC GUCCUUGUGG CGUCGCUGAA CCAUAGCAGG CUAGCAACGG UGCACUUGGC GGAAAGGCCU UGGGUGCUUG CUGGCGAAUU GCAAUGUCAU UUUGCGUGGG GAUAAAUCAU UUGUAUACGA CUUAGAUGUA CAACGGGGUA UUGUAAGCAG UAGAGUAGCC UUGUUGUUAC GAUCUGCUGA GAUUAAGCCU UUGUUGUCUG AUUUGU
MassTheoretical: 1.097493875 MDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

+
Component #54: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUUGCGGCC AUAUCUACCA GAAAGCACCG UUUCCCGUCC GAUCAACUGU AGUUAAGCUG GUAAGAGCCU GACCGAGUAG UGUAGUGGGU GACCAUACGC GAAACUCAGG UGCUGCAAUC U
MassTheoretical: 38.951105 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

+
Component #55: protein, Probable metalloprotease ARX1

ProteinName: Probable metalloprotease ARX1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.290336 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #56: protein, rRNA-processing protein CGR1

ProteinName: rRNA-processing protein CGR1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.460057 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #57: protein, Exosome complex exonuclease RRP6

ProteinName: Exosome complex exonuclease RRP6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 84.16057 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #58: protein, Exosome complex protein LRP1

ProteinName: Exosome complex protein LRP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.086297 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #59: protein, ATP-dependent RNA helicase DOB1

ProteinName: ATP-dependent RNA helicase DOB1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 115.230648 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #60: protein, MPP6

ProteinName: MPP6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.954168 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #61: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #62: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

+
Component #63: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: OTHER

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 38.4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 22439
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
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