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- EMDB-8143: nuclear ribo-nucleoprotein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-8143
Titlenuclear ribo-nucleoprotein complex
Map dataNone
Sample
  • Complex: nuclear ribo-nucleoprotein complex
Function / homology
Function and homology information


tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / tRNA acetylation / t-UTP complex / nuclear microtubule / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity ...tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / tRNA acetylation / t-UTP complex / nuclear microtubule / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D methylation guide snoRNP complex / rRNA primary transcript binding / rRNA base methylation / ribonuclease P activity / tRNA 5'-leader removal / rRNA methylation / histone H2A Q104 methyltransferase activity / U3 snoRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / tRNA processing / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / snoRNA binding / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of transcription by RNA polymerase I / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / RNA nuclease activity / ribosomal subunit export from nucleus / regulation of translational fidelity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / enzyme activator activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / small-subunit processome / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Archaeal Nop5/56-rel, N-terminal domain / : / : / HEATR1-like, HEAT repeats / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain ...: / Archaeal Nop5/56-rel, N-terminal domain / : / : / HEATR1-like, HEAT repeats / 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 / rRNA-processing protein Fcf1, PIN domain / rRNA-processing protein Fcf1/Utp23 / Fcf1 / BP28, C-terminal domain / RNA 3'-terminal phosphate cyclase-like, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosome biogenesis protein Bms1, N-terminal / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / RNA 3'-terminal phosphate cyclase signature. / BP28CT (NUC211) domain / Small-subunit processome, Utp21 / RNA 3'-terminal phosphate cyclase type 2 / Utp21 specific WD40 associated putative domain / Ribosomal RNA-processing protein Rrp9-like / RNA 3'-terminal phosphate cyclase / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Nucleolar protein Nop56/Nop58 / Krr1, KH1 domain / Krr1 KH1 domain / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / U3 snoRNP protein/Ribosome production factor 1 / Large family of predicted nucleotide-binding domains / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / Anaphase-promoting complex subunit 4, WD40 domain / PIN domain / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Anaphase-promoting complex subunit 4 WD40 domain / Ribosomal protein L7Ae, archaea / Brix domain / Brix domain / Brix domain profile. / Brix / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / K Homology domain, type 1 superfamily / PIN-like domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / GNAT domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal
Similarity search - Domain/homology
C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / 40S ribosomal protein S6 / RNA cytidine acetyltransferase / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 10 / Uncharacterized protein / Uncharacterized protein / PIN domain-containing protein / U3 small nucleolar ribonucleoprotein protein IMP4 / 40S ribosomal protein S24 ...C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / 40S ribosomal protein S6 / RNA cytidine acetyltransferase / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 10 / Uncharacterized protein / Uncharacterized protein / PIN domain-containing protein / U3 small nucleolar ribonucleoprotein protein IMP4 / 40S ribosomal protein S24 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL8 / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / rRNA processing protein RCL1 / Ribosome biogenesis protein BMS1 / 40S ribosomal protein S8 / 40S ribosomal protein S11, putative / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsKornprobst M / Turk M / Kellner N / Cheng J / Flemming D / Kos-Braun IC / Kos M / Thoms M / Berninghausen O / Beckmann R / Hurt E
CitationJournal: Cell / Year: 2016
Title: Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome.
Authors: Markus Kornprobst / Martin Turk / Nikola Kellner / Jingdong Cheng / Dirk Flemming / Isabelle Koš-Braun / Martin Koš / Matthias Thoms / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that ...The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding.
History
DepositionApr 5, 2016-
Header (metadata) releaseAug 3, 2016-
Map releaseAug 3, 2016-
UpdateAug 3, 2016-
Current statusAug 3, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5jpq
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5jpq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8143.png

Downloads & links

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Map

FileDownload / File: emd_8143.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.05605118 - 0.10664072
Average (Standard dev.)-0.000251965 (±0.006865005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 478.464 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0681.0681.068
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z478.464478.464478.464
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ329329329
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.0560.107-0.000

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Supplemental data

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Sample components

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Entire : nuclear ribo-nucleoprotein complex

EntireName: nuclear ribo-nucleoprotein complex
Components
  • Complex: nuclear ribo-nucleoprotein complex

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Supramolecule #1: nuclear ribo-nucleoprotein complex

SupramoleculeName: nuclear ribo-nucleoprotein complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chaetomium thermophilum (fungus)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.66 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43116
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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