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- EMDB-4301: Structure of the nuclear RNA exosome -

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Entry
Database: EMDB / ID: 4301
TitleStructure of the nuclear RNA exosome
Map dataStructure of the nuclear RNA exosome
SampleNuclear RNA exosome
  • nucleic acid
  • nucleic-acidNucleic acid
  • (Exosome complex component ...) x 9
  • (Exosome complex exonuclease ...) x 2
  • Exosome complex protein LRP1
  • ATP-dependent RNA helicase DOB1
  • M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog
Function / homologyPIN domain / Exosome-associated factor Rrp47/DNA strand repair C1D / Helicase superfamily 1/2, ATP-binding domain / ATP-dependent RNA helicase Ski2, C-terminal / Exosome-associated factor Rrp6, N-terminal / Nucleic acid-binding, OB-fold / Ribonuclease H-like superfamily / DEAD/DEAH box helicase domain / Prismane-like superfamily / HRDC-like superfamily ...PIN domain / Exosome-associated factor Rrp47/DNA strand repair C1D / Helicase superfamily 1/2, ATP-binding domain / ATP-dependent RNA helicase Ski2, C-terminal / Exosome-associated factor Rrp6, N-terminal / Nucleic acid-binding, OB-fold / Ribonuclease H-like superfamily / DEAD/DEAH box helicase domain / Prismane-like superfamily / HRDC-like superfamily / ATP-dependent RNA helicase Ski2-like / Sas10/Utp3/C1D / K Homology domain, type 1 / S1 domain / 3'-5' exonuclease domain / HRDC domain / Ribonuclease II/R / Helicase, C-terminal / Exoribonuclease, phosphorolytic domain 1 / Exoribonuclease, phosphorolytic domain 2 / M-phase phosphoprotein 6 / RNB domain / Exosome complex component RRP45 / DEAD/DEAH box helicase / Exosome complex component Csl4 / Rrp40, S1 domain / K Homology domain, type 1 superfamily / Exoribonuclease, PH domain 2 superfamily / Rrp44-like cold shock domain / Exosome complex exonuclease RRP44, S1 domain / Exosome complex component Rrp43 / PIN-like domain superfamily / Exosome complex component CSL4, C-terminal / P-loop containing nucleoside triphosphate hydrolase / PNPase/RNase PH domain superfamily / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Exosome complex component, N-terminal domain / rRNA-processing arch domain / RNA-binding domain, S1 / Ribonuclease II/R, conserved site / Ribosomal protein S5 domain 2-type fold / HRDC domain / Helicase conserved C-terminal domain / 3' exoribonuclease family, domain 2 / S1 domain profile. / DSHCT (NUC185) domain / M-phase phosphoprotein 6 / Exosome component EXOSC1/CSL4 / rRNA-processing arch domain / PIN domain / Exosome complex exonuclease RRP4 N-terminal region / 3'-5' exonuclease / 3' exoribonuclease family, domain 1 / KH domain / S1 domain / Rrp44-like cold shock domain / Ribonuclease II family signature. / Sas10/Utp3/C1D family / PMC2NT (NUC016) domain / HRDC domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA decay by 3' to 5' exoribonuclease / Superfamilies 1 and 2 helicase C-terminal domain profile. / regulation of exoribonuclease activity / ncRNA polyadenylation / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / ncRNA 3'-end processing / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / maturation of 5.8S rRNA / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear polyadenylation-dependent CUT catabolic process / nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' / nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription / U1 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear retention of pre-mRNA at the site of transcription / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / CUT catabolic process / nuclear polyadenylation-dependent tRNA catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / nuclear exosome (RNase complex) / exosome (RNase complex) / histone mRNA catabolic process / U4 snRNA 3'-end processing / polyadenylation-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear mRNA surveillance / nuclear-transcribed mRNA catabolic process, non-stop decay / Hydrolases, Acting on ester bonds, Endoribonucleases producing 5'-phosphomonoesters / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / rRNA metabolic process / ATP-dependent 3'-5' RNA helicase activity / exonucleolytic catabolism of deadenylated mRNA / rRNA catabolic process
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / 4.6 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: 6fsz

SummaryFull reportAbout validation report
DateDeposition: Feb 20, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Mar 21, 2018 / Last update: Apr 25, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6fsz
  • Surface level: 0.035
  • 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_4301.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:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.047356263 - 0.11682776
Average (Standard dev.)0.00011799472 (0.00213669)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions440440440
Origin0.00.00.0
Limit439.0439.0439.0
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-0.0470.1170.000

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Supplemental data

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Sample components

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Entire Nuclear RNA exosome

EntireName: Nuclear RNA exosome / Number of components: 18

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Component #1: protein, Nuclear RNA exosome

ProteinName: Nuclear RNA exosome / Recombinant expression: No

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Component #2: protein, Nuclear RNA exosome

ProteinName: Nuclear RNA exosome / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, nucleic acid

ProteinName: nucleic acid / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #4: nucleic-acid, RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*...

Nucleic-acidName: RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAAAUUUAAA UUUUUUUUUU UUU
MassTheoretical: 7.158137 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #5: protein, Exosome complex component RRP45

ProteinName: Exosome complex component RRP45 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.79959 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Exosome complex component SKI6

ProteinName: Exosome complex component SKI6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.794926 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Exosome complex component RRP43

ProteinName: Exosome complex component RRP43 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.977805 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Exosome complex component RRP46

ProteinName: Exosome complex component RRP46 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.913988 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, Exosome complex component RRP42

ProteinName: Exosome complex component RRP42 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.294398 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #10: protein, Exosome complex component MTR3

ProteinName: Exosome complex component MTR3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.559869 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: protein, Exosome complex component RRP40

ProteinName: Exosome complex component RRP40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.778551 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #12: protein, Exosome complex component RRP4

ProteinName: Exosome complex component RRP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.714445 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #13: protein, Exosome complex component CSL4

ProteinName: Exosome complex component CSL4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.805645 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #14: protein, Exosome complex exonuclease DIS3

ProteinName: Exosome complex exonuclease DIS3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 113.983898 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #15: protein, Exosome complex exonuclease RRP6

ProteinName: Exosome complex exonuclease RRP6 / Details: Inactive point mutant D296N / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 84.159586 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #16: 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)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #17: protein, ATP-dependent RNA helicase DOB1

ProteinName: ATP-dependent RNA helicase DOB1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 122.260094 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #18: protein, M-phase phosphoprotein 6 homolog,M-phase phosphoprotein ...

ProteinName: M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog
Details: Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.101711 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

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

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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)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 22439
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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