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

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Entry
Database: EMDB / ID: EMD-11809
TitleCryo-EM structure of the 90S-exosome super-complex (state Post-A1-exosome, Dhr1-Dim1)
Map data
Sample90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1 sample
Function / homology
Function and homology information


ncRNA polyadenylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / ncRNA 3'-end processing / rRNA acetylation involved in maturation of SSU-rRNA / TRAMP complex / mRNA decay by 3' to 5' exoribonuclease / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription ...ncRNA polyadenylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / ncRNA 3'-end processing / rRNA acetylation involved in maturation of SSU-rRNA / TRAMP complex / mRNA decay by 3' to 5' exoribonuclease / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription / nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / U1 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / tRNA acetylation / mRNA modification / nuclear polyadenylation-dependent tRNA catabolic process / sno(s)RNA processing / CURI complex / nuclear polyadenylation-dependent rRNA catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / RNA fragment catabolic process / t-UTP complex / CUT catabolic process / U4 snRNA 3'-end processing / exosome (RNase complex) / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 3'-5' RNA helicase activity / Pwp2p-containing subcomplex of 90S preribosome / nuclear exosome (RNase complex) / histone-glutamine methyltransferase activity / polyadenylation-dependent snoRNA 3'-end processing / box C/D RNA binding / box C/D RNA 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) / Mpp10 complex / septum digestion after cytokinesis / rRNA methyltransferase activity / nuclear-transcribed mRNA catabolic process, non-stop decay / nuclear mRNA surveillance / rRNA (pseudouridine) methyltransferase activity / box H/ACA snoRNA binding / rRNA modification / rRNA 2'-O-methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / regulation of transcription by RNA polymerase I / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / 90S preribosome assembly / rDNA heterochromatin / exonucleolytic catabolism of deadenylated mRNA / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nonfunctional rRNA decay / snRNA binding / rRNA catabolic process / box C/D RNP complex / rRNA metabolic process / tRNA export from nucleus / rRNA base methylation / rRNA primary transcript binding / positive regulation of transcription by RNA polymerase I / single-stranded telomeric DNA binding / protein localization to nucleolus / SUMOylation of RNA binding proteins / sno(s)RNA-containing ribonucleoprotein complex / mTORC1-mediated signalling / maturation of 5.8S rRNA / histone glutamine methylation / U4 snRNA binding / poly(A) binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / U3 snoRNA binding / RNA catabolic process / Cul4-RING E3 ubiquitin ligase complex / rRNA export from nucleus / : / poly(A)+ mRNA export from nucleus / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / O-methyltransferase activity / 90S preribosome / preribosome, small subunit precursor / precatalytic spliceosome / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / snoRNA binding / GTP hydrolysis and joining of the 60S ribosomal subunit / rRNA methylation / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / poly(U) RNA binding / mRNA catabolic process
Similarity search - Function
Regular of rDNA transcription protein 14 / Regulator of rDNA transcription 14 / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / Exosome complex component Rrp43 / Exosome complex component RRP45 / Rrp44-like cold shock domain / Rrp40, S1 domain ...Regular of rDNA transcription protein 14 / Regulator of rDNA transcription 14 / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / Exosome complex component Rrp43 / Exosome complex component RRP45 / Rrp44-like cold shock domain / Rrp40, S1 domain / Rrp44-like cold shock domain / Exosome complex component, N-terminal domain / Exosome complex exonuclease RRP4 N-terminal region / Exosome component EXOSC1/CSL4 / Exosome complex component Csl4 / Exosome complex component CSL4, C-terminal / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / PIN domain / Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis antagonizing transcription factor / Protein AATF/Bfr2 / rRNA-processing arch domain / DSHCT (NUC185) domain / Nucleolar protein 10/Enp2 / NUC153 domain / ATP-dependent RNA helicase Ski2-like / ATP-dependent RNA helicase Ski2, C-terminal / Exosome complex RNA-binding protein 1/RRP40/RRP4 / NUC153 / rRNA-processing arch domain / DSHCT / KH domain / U3 small nucleolar RNA-associated protein 8 / Utp8 family / Ribonuclease II family signature. / Ribonuclease II/R, conserved site / Ribonuclease II/R / RNB domain / RNB / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / TmcA/NAT10/Kre33 / GNAT acetyltransferase 2 / Helicase / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / Ribosomal RNA assembly KRR1 / U3 snoRNA associated / Down-regulated in metastasis / Down-regulated-in-metastasis protein / U3 snoRNA associated / Nucleolar complex protein 4 / CCAAT-binding factor / CBF/Mak21 family / Nop14-like family / Nucleolar protein 14 / rRNA-processing protein Fcf1, PIN domain / Fcf2 pre-rRNA processing / Nrap protein domain 1 / Nrap protein domain 1 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein domain 3 / Nrap protein PAP/OAS-like domain / Utp11 protein / Fcf2 pre-rRNA processing, C-terminal / Nrap protein, domain 3 / Sof1-like domain / BING4CT (NUC141) domain / BING4CT (NUC141) domain / Nrap protein, domain 2 / BING4, C-terminal domain / Nrap protein, domain 4 / WD repeat-containing protein WDR46/Utp7 / Nrap protein, domain 5 / Nrap protein, domain 6 / NOL6/Upt22 / Nrap protein PAP/OAS1-like domain 5 / Small-subunit processome, Utp11 / Nrap protein domain 6 / Sof1-like protein / Fcf2/DNTTIP2 / Ribosomal RNA-processing protein 7 / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Fcf1 / rRNA-processing protein Fcf1/Utp23 / Rrp7, RRM-like N-terminal domain / Rrp7 RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 6 / UTP15 C terminal / U3 small nucleolar RNA-associated protein 15, C-terminal / Small-subunit processome, Utp14 / Sas10 C-terminal domain / Sas10 C-terminal domain
Similarity search - Domain/homology
U3 small nucleolar RNA-associated protein 13 / Exosome complex component RRP45 / rRNA-processing protein FCF1 / rRNA biogenesis protein RRP5 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar RNA-associated protein 5 / NET1-associated nuclear protein 1 / Ribosomal RNA small subunit methyltransferase NEP1 ...U3 small nucleolar RNA-associated protein 13 / Exosome complex component RRP45 / rRNA-processing protein FCF1 / rRNA biogenesis protein RRP5 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar RNA-associated protein 5 / NET1-associated nuclear protein 1 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar ribonucleoprotein protein IMP4 / RNA cytidine acetyltransferase / Exosome complex component CSL4 / U3 small nucleolar RNA-associated protein 8 / Exosome complex component RRP46 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 21 / Protein BFR2 / Ribosomal RNA-processing protein 9 / U3 small nucleolar RNA-associated protein 12 / Ribosome biogenesis protein ENP2 / Nucleolar complex protein 14 / 40S ribosomal protein S28-A / Nucleolar protein 58 / Nucleolar protein 56 / Exosome complex component RRP42 / Something about silencing protein 10 / Nucleolar complex protein 4 / rRNA-processing protein FCF2 / Ribosome biogenesis protein BMS1 / Bud site selection protein 21 / Exosome complex component RRP40 / Exosome complex exonuclease DIS3 / RNA 3'-terminal phosphate cyclase-like protein / U3 small nucleolar RNA-associated protein 4 / Exosome complex component MTR3 / 40S ribosomal protein S8-A / U3 small nucleolar RNA-associated protein MPP10 / 40S ribosomal protein S11-A / KRR1 small subunit processome component / Ribosomal RNA-processing protein 7 / Exosome complex component RRP43 / rRNA 2'-O-methyltransferase fibrillarin / 40S ribosomal protein S18-A / 40S ribosomal protein S16-A / 40S ribosomal protein S6-A / 40S ribosomal protein S5 / 40S ribosomal protein S4-A / 40S ribosomal protein S24-A / 40S ribosomal protein S23-A / 40S ribosomal protein S22-A / 40S ribosomal protein S14-A / 40S ribosomal protein S13 / 40S ribosomal protein S9-A / Periodic tryptophan protein 2 / 40S ribosomal protein S7-A / ATP-dependent RNA helicase DOB1 / U3 small nucleolar RNA-associated protein 9 / Exosome complex component SKI6 / U3 small nucleolar RNA-associated protein 10 / Protein FAF1 / Regulator of rDNA transcription protein 14 / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 7 / 13 kDa ribonucleoprotein-associated protein / Exosome complex component RRP4 / U3 small nucleolar ribonucleoprotein protein IMP3 / Essential nuclear protein 1 / Ribosome biogenesis protein UTP30 / 40S ribosomal protein S27-A / U3 small nucleolar RNA-associated protein 20 / U3 small nucleolar RNA-associated protein 11 / Protein SOF1 / 40S ribosomal protein S1-A / Pre-rRNA-processing protein PNO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker'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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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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)
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
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
Number of Components: 1

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Component #1: protein, 90S-exosome super-complex in state Post-A1-exosome from ...

ProteinName: 90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1 sample
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen Name: ETHANE

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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: 44 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: 3892
3D reconstructionResolution: 7.5 Å / Resolution Method: FSC 0.143 CUT-OFF / Euler angles: Relion
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Input PDB model: 6ZQD

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