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- EMDB-11809: Cryo-EM structure of the 90S-exosome super-complex (state Post-A1... -

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Basic information

Entry
Database: EMDB / ID: EMD-11809
TitleCryo-EM structure of the 90S-exosome super-complex (state Post-A1-exosome, Dhr1-Dim1)
Map datalocal resolution filtered map
Sample
  • Complex: 90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1 sample
Function / homology
Function and homology information


mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear polyadenylation-dependent mRNA catabolic process / tRNA wobble cytosine modification / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / regulation of ribosomal protein gene transcription by RNA polymerase II / box H/ACA snoRNA binding ...mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear polyadenylation-dependent mRNA catabolic process / tRNA wobble cytosine modification / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / regulation of ribosomal protein gene transcription by RNA polymerase II / box H/ACA snoRNA binding / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / U1 snRNA 3'-end processing / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / nuclear polyadenylation-dependent CUT catabolic process / RNA fragment catabolic process / U5 snRNA 3'-end processing / tRNA acetylation / rRNA 2'-O-methylation / TRAMP-dependent tRNA surveillance pathway / CURI complex / UTP-C complex / CUT catabolic process / exosome (RNase complex) / U4 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / nuclear microtubule / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / nuclear exosome (RNase complex) / rRNA (pseudouridine) methyltransferase activity / nuclear-transcribed mRNA catabolic process, non-stop decay / rRNA modification / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of rRNA processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / septum digestion after cytokinesis / snRNA binding / tRNA re-export from nucleus / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / 3'-5' RNA helicase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / nuclear mRNA surveillance / rRNA catabolic process / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / box C/D methylation guide snoRNP complex / U4/U6 snRNP / positive regulation of rRNA processing / tRNA export from nucleus / single-stranded telomeric DNA binding / poly(A) binding / mRNA 3'-UTR AU-rich region binding / rRNA primary transcript binding / rRNA base methylation / sno(s)RNA-containing ribonucleoprotein complex / Negative regulators of DDX58/IFIH1 signaling / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / O-methyltransferase activity / 90S preribosome assembly / rRNA methylation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / histone H2AQ104 methyltransferase activity / mTORC1-mediated signalling / Protein hydroxylation / mRNA modification / U4 snRNP / U3 snoRNA binding / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / snoRNA binding / precatalytic spliceosome / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / maturation of 5.8S rRNA / nonfunctional rRNA decay / establishment of cell polarity / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA catabolic process / nucleolar large rRNA transcription by RNA polymerase I
Similarity search - Function
: / Exosome complex component CSL4, N-terminal domain / Regulator of rDNA transcription 14 / Regular of rDNA transcription protein 14 / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Exosome complex exonuclease RRP44, S1 domain / Protein AATF/Bfr2 ...: / Exosome complex component CSL4, N-terminal domain / Regulator of rDNA transcription 14 / Regular of rDNA transcription protein 14 / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Exosome complex exonuclease RRP44, S1 domain / Protein AATF/Bfr2 / : / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis antagonizing transcription factor / S1 domain / PIN domain / NUC153 / Nucleolar protein 10/Enp2 / : / : / NUC153 domain / Nucleolar protein 10-like, second domain / Nucleolar protein 10-like, N-terminal domain / U3 small nucleolar RNA-associated protein 8 / Exosome complex component RRP45 / Rrp40, S1 domain / : / : / Utp8, N-terminal beta propeller / Exosome complex component RRP40, S1 domain / Utp8, C-terminal / rRNA biogenesis protein Rrp5 / : / : / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 snoRNA associated / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 20, C-terminal / : / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 snoRNA associated / U3 small nucleolar RNA-associated protein 20 domain / Small subunit processome component 20 homolog, C-terminal / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10/TcmA, helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / Nucleolar protein 14 / Nop14-like family / WD repeat-containing protein 75 second beta-propeller / : / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Nrap protein domain 1 / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 6 / U3 small nucleolar RNA-associated protein 6 / Ribonuclease II/R, conserved site / Ribosomal RNA-processing protein 7, C-terminal domain / rRNA-processing arch domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 4 / : / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / Ribonuclease II family signature. / Small-subunit processome, Utp11 / Sof1-like protein
Similarity search - Domain/homology
Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A ...Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / rRNA 2'-O-methyltransferase fibrillarin / Exosome complex component RRP43 / Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / Periodic tryptophan protein 2 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS7A / U3 small nucleolar ribonucleoprotein protein IMP3 / Small ribosomal subunit protein eS1A / Protein SOF1 / U3 small nucleolar RNA-associated protein 11 / U3 small nucleolar RNA-associated protein 20 / Small ribosomal subunit protein eS27A / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / Exosome complex component RRP4 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar RNA-associated protein 18 / Regulator of rDNA transcription protein 14 / Protein FAF1 / U3 small nucleolar RNA-associated protein 10 / Exosome complex component SKI6 / ATP-dependent RNA helicase DOB1 / U3 small nucleolar RNA-associated protein MPP10 / Ribosome biogenesis protein ENP2 / Exosome complex component MTR3 / U3 small nucleolar RNA-associated protein 22 / Exosome complex component RRP46 / U3 small nucleolar RNA-associated protein 8 / Exosome complex component CSL4 / RNA cytidine acetyltransferase / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 6 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 14 / rRNA biogenesis protein RRP5 / rRNA-processing protein FCF1 / Exosome complex component RRP45 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / Protein BFR2 / U3 small nucleolar RNA-associated protein 4 / rRNA processing protein RCL1 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 / U3 small nucleolar RNA-associated protein 16 / Ribosome biogenesis protein BMS1 / rRNA-processing protein FCF2 / Something about silencing protein 10 / U3 small nucleolar RNA-associated protein 12 / Exosome complex component RRP42 / Nucleolar protein 56 / Nucleolar protein 58 / Small ribosomal subunit protein eS28A / Nucleolar complex protein 14 / Pre-rRNA-processing protein PNO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsCheng J / Lau B / Venuta GL / Berninghausen O / Beckmann R / Hurt E
CitationJournal: Mol Cell / Year: 2021
Title: Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome.
Authors: Benjamin Lau / Jingdong Cheng / Dirk Flemming / Giuseppe La Venuta / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in ...Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in this progression is removal of the 5' external transcribed spacer (5'-ETS), an RNA extension at the 18S rRNA that is integrated into the huge 90S pre-ribosome structure. Upon endo-nucleolytic cleavage at an internal site, A, the 5'-ETS is separated from the 18S rRNA and degraded. Here we present biochemical and cryo-electron microscopy analyses that depict the RNA exosome, a major 3'-5' exoribonuclease complex, in a super-complex with the 90S pre-ribosome. The exosome is docked to the 90S through its co-factor Mtr4 helicase, a processive RNA duplex-dismantling helicase, which strategically positions the exosome at the base of 5'-ETS helices H9-H9', which are dislodged in our 90S-exosome structures. These findings suggest a direct role of the exosome in structural remodeling of the 90S pre-ribosome to drive eukaryotic ribosome synthesis.
History
DepositionSep 29, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11809.png

Downloads & links

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Map

FileDownload / File: emd_11809.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 480 pix.
= 508.32 Å		1.06 Å/pix.
x 480 pix.
= 508.32 Å		1.06 Å/pix.
x 480 pix.
= 508.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.077466756 - 0.12347478
Average (Standard dev.)0.00076612557 (±0.0045423233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 508.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z508.320508.320508.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0770.1230.001

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Supplemental data

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Sample components

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Entire : 90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1...

EntireName: 90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1 sample
Components
  • Complex: 90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1 sample

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Supramolecule #1: 90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1...

SupramoleculeName: 90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1 sample
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#77
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3892
Initial angle assignmentType: OTHER / Details: Relion
Final angle assignmentType: OTHER / Details: Relion
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6zqd

RefinementProtocol: RIGID BODY FIT

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