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- EMDB-8143: nuclear ribo-nucleoprotein complex -

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Basic information

Entry
Database: EMDB / ID: 8143
Titlenuclear ribo-nucleoprotein complex
Map data
Samplenuclear ribo-nucleoprotein complex:
Function / homologyRibosomal protein S7 domain / PIN-like domain superfamily / 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 L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily ...Ribosomal protein S7 domain / PIN-like domain superfamily / 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 L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / S-adenosyl-L-methionine-dependent methyltransferase / RNA 3'-terminal phosphate cyclase domain / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Ribosomal protein S8 superfamily / Nop domain superfamily / WD40-repeat-containing domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Ribosomal RNA assembly KRR1 / Ribosomal protein L1-like / Ribosomal protein S7 domain superfamily / Ribosomal protein S6e, conserved site / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / Ribosomal protein L1, 3-layer alpha/beta-sandwich / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S15P / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / 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 / K Homology domain, type 1 superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / RS4NT (NUC023) domain / S4 domain / snoRNA binding domain, fibrillarin / EMG1/NEP1 methyltransferase / Utp21 specific WD40 associated putative domain / Brix domain / Fcf1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / Helicase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Ribosomal S13/S15 N-terminal domain / AARP2CN (NUC121) domain / Fibrillarin / BP28CT (NUC211) domain / Domain of unknown function (DUF1726) / U3 small nucleolar RNA-associated protein 10 / Anaphase-promoting complex subunit 4 WD40 domain / GNAT acetyltransferase 2 / Possible tRNA binding domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S24e / Ribosomal protein S7e / RNA-binding S4 domain superfamily / Ribosomal protein S15 / RNA 3'-terminal phosphate cyclase domain superfamily / rRNA-processing protein Fcf1, PIN domain / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal protein S4e, central domain superfamily / Ribosomal RNA-processing protein Rrp9-like / Ribosome biogenesis protein Bms1/Tsr1 / U3 small nucleolar RNA-associated protein 10 / ATPase family associated with various cellular activities (AAA) / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S17 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S9/S16 / WD domain, G-beta repeat / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein L1p/L10e family / Ribosomal family S4e / Ribosomal S3Ae family
Function and homology information
SourceChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / cryo EM / 7.3 Å resolution
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 ReportPDB-ID: 5jpq

SummaryFull reportAbout validation report
DateDeposition: Apr 5, 2016 / Header (metadata) release: Aug 3, 2016 / Map release: Aug 3, 2016 / Last update: Aug 3, 2016

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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 models: PDB-5jpq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8143.map.gz (map file in CCP4 format, 359662 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
448 pix
1.07 Å/pix.
= 478.464 Å
448 pix
1.07 Å/pix.
= 478.464 Å
448 pix
1.07 Å/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 Level:0.025 (by author), 0.025 (movie #1):
Minimum - Maximum-0.05605118 - 0.10664072
Average (Standard dev.)-0.000251965 (0.006865005)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions448448448
Origin0.00.00.0
Limit447.0447.0447.0
Spacing448448448
CellA=B=C: 478.464 Å
α=β=γ: 90.0 deg.

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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