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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 data
Samplenuclear ribo-nucleoprotein complex
Function / homology
Function and homology information


rRNA cytidine N-acetyltransferase activity / tRNA acetylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA small subunit pseudouridine methyltransferase Nep1 / histone-glutamine methyltransferase activity / mRNA modification / box C/D RNA 3'-end processing / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA modification ...rRNA cytidine N-acetyltransferase activity / tRNA acetylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA small subunit pseudouridine methyltransferase Nep1 / histone-glutamine methyltransferase activity / mRNA modification / box C/D RNA 3'-end processing / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA modification / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex / rRNA base methylation / histone glutamine methylation / ribonuclease P activity / tRNA 5'-leader removal / U3 snoRNA binding / rRNA export from nucleus / 90S preribosome / preribosome, small subunit precursor / tRNA processing / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / snoRNA binding / 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) / maturation of SSU-rRNA / regulation of translational fidelity / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / maturation of LSU-rRNA / endoribonuclease activity / positive regulation of translational fidelity / enzyme activator activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / rRNA processing / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / cytosolic large ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Ribosomal protein L23/L15e core domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / AARP2CN / BP28, C-terminal domain / NOSIC / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / S15/NS1, RNA-binding ...Ribosomal protein L23/L15e core domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / AARP2CN / BP28, C-terminal domain / NOSIC / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / S15/NS1, RNA-binding / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Quinoprotein alcohol dehydrogenase-like superfamily / Helicase domain / WD40-repeat-containing domain / Ribosomal protein L7Ae conserved site / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S11 / Ribosomal protein S24e / Nop domain / PIN domain / RNA-binding S4 domain / ATPase, AAA-type, core / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Small-subunit processome, Utp21 / K Homology domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / rRNA-processing protein Fcf1/Utp23 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Brix domain / RNA 3'-terminal phosphate cyclase type 2 / Ribosomal protein S4, conserved site / Ribosomal protein S3Ae / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal RNA assembly KRR1 / Anaphase-promoting complex subunit 4, WD40 domain / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Possible tRNA binding domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / RNA 3'-terminal phosphate cyclase domain / Helix hairpin bin domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PIN-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal S24e conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S15P / Ribosomal protein S7, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Fibrillarin, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L7Ae, archaea / Ribosomal protein S4/S9 / WD40 repeat / Ribosomal protein S6e / 40S ribosomal protein S11, N-terminal / RNA 3'-terminal phosphate cyclase domain superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S8e / WD40-repeat-containing domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosome biogenesis protein Bms1, N-terminal / TmcA/NAT10/Kre33 / Ribosomal protein S4e, central domain superfamily / Ribosomal RNA-processing protein Rrp9-like / Ribosome biogenesis protein Bms1/Tsr1 / U3 small nucleolar RNA-associated protein 10 / Krr1, KH1 domain / Ribosomal protein S4, KOW domain / Nop, C-terminal domain / Ribosomal protein S8e subdomain, eukaryotes / RNA cytidine acetyltransferase NAT10 / Nop domain superfamily
40S ribosomal protein S4 / 40S ribosomal protein S3a / 40S ribosomal protein S11, putative / 40S ribosomal protein S8 / Ribosome biogenesis protein BMS1 / RNA 3'-terminal phosphate cyclase-like protein / Ribosomal RNA-processing protein 9 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 21 / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ...40S ribosomal protein S4 / 40S ribosomal protein S3a / 40S ribosomal protein S11, putative / 40S ribosomal protein S8 / Ribosome biogenesis protein BMS1 / RNA 3'-terminal phosphate cyclase-like protein / Ribosomal RNA-processing protein 9 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 21 / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 50S ribosomal protein L7Ae / 40S ribosomal protein S5 / 40S ribosomal protein S16-A / U3 small nucleolar RNA-associated protein 10 / 40S ribosomal protein S22-A / 40S ribosomal protein S14-A / 40S ribosomal protein S13 / 40S ribosomal protein S9-A / 40S ribosomal protein S7 / 40S ribosomal protein S24 / Putative U3 small nucleolar ribonucleoprotein / PINc domain-containing protein / S4 RNA-binding domain-containing protein / Uncharacterized protein / KRR1 small subunit processome component / RNA cytidine acetyltransferase / 40S ribosomal protein S6 / C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / 40S ribosomal protein S28-A
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.
Validation ReportSummary, Full report, XML, About validation report
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

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)
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
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 / Number of components: 1

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Component #1: protein, nuclear ribo-nucleoprotein complex

ProteinName: nuclear ribo-nucleoprotein complex / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (fungus)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
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: 2.66 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 43116
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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