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- EMDB-8223: Random conical tilt reconstruction of Saccharomyces cerevisiae UtpB -

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Basic information

Entry
Database: EMDB / ID: EMD-8223
TitleRandom conical tilt reconstruction of Saccharomyces cerevisiae UtpB
Map dataSaccharomyces cerevisiae UtpB
Sample
  • Complex: Saccharomyces cerevisiae UtpB
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsBarandun J / Hunziker M / Tan D / Kim KH / Walz T / Klinge S
Funding support United States, Canada, United Kingdom, 13 items
OrganizationGrant numberCountry
Irma T. Hirschl Trust United States
Alfred P. Sloan Foundation United States
Human Frontier Science Program
Alexandrine and Alexander L. Sinsheimer Fund United States
European Molecular Biology Organization (EMBO) Short-term fellowshipASTF 352-2015
Canadian Institutes of Health Research (CIHR) Canada
European Molecular Biology Organization (EMBO) Long-term fellowshipALTF 51-2014
Wellcome Trust097383 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)PHS GM103314 and PHS GM109824 United States
Biotechnology and Biological Sciences Research Council (BBSRC)BB/F010656/1 United Kingdom
FEBS long-term fellowship
Robertson Foundation United States
Fonds de Recherche du Quebec-Sante (FRQ-S) Canada
CitationJournal: Nat Commun / Year: 2016
Title: UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly.
Authors: Mirjam Hunziker / Jonas Barandun / Elisabeth Petfalski / Dongyan Tan / Clémentine Delan-Forino / Kelly R Molloy / Kelly H Kim / Hywel Dunn-Davies / Yi Shi / Malik Chaker-Margot / Brian T ...Authors: Mirjam Hunziker / Jonas Barandun / Elisabeth Petfalski / Dongyan Tan / Clémentine Delan-Forino / Kelly R Molloy / Kelly H Kim / Hywel Dunn-Davies / Yi Shi / Malik Chaker-Margot / Brian T Chait / Thomas Walz / David Tollervey / Sebastian Klinge /
Abstract: Early eukaryotic ribosome biogenesis involves large multi-protein complexes, which co-transcriptionally associate with pre-ribosomal RNA to form the small subunit processome. The precise mechanisms ...Early eukaryotic ribosome biogenesis involves large multi-protein complexes, which co-transcriptionally associate with pre-ribosomal RNA to form the small subunit processome. The precise mechanisms by which two of the largest multi-protein complexes-UtpA and UtpB-interact with nascent pre-ribosomal RNA are poorly understood. Here, we combined biochemical and structural biology approaches with ensembles of RNA-protein cross-linking data to elucidate the essential functions of both complexes. We show that UtpA contains a large composite RNA-binding site and captures the 5' end of pre-ribosomal RNA. UtpB forms an extended structure that binds early pre-ribosomal intermediates in close proximity to architectural sites such as an RNA duplex formed by the 5' ETS and U3 snoRNA as well as the 3' boundary of the 18S rRNA. Both complexes therefore act as vital RNA chaperones to initiate eukaryotic ribosome assembly.
History
DepositionMay 27, 2016-
Header (metadata) releaseJul 6, 2016-
Map releaseJul 6, 2016-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0645
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0645
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8223.png

Downloads & links

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Map

FileDownload / File: emd_8223.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSaccharomyces cerevisiae UtpB
Voxel sizeX=Y=Z: 2.61 Å
Density
Contour LevelBy AUTHOR: 0.0645 / Movie #1: 0.0645
Minimum - Maximum-0.60342336 - 0.90822613
Average (Standard dev.)-0.0015196986 (±0.029405123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 501.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.612.612.61
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z501.120501.120501.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.6030.908-0.002

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Supplemental data

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Sample components

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Entire : Saccharomyces cerevisiae UtpB

EntireName: Saccharomyces cerevisiae UtpB
Components
  • Complex: Saccharomyces cerevisiae UtpB

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Supramolecule #1: Saccharomyces cerevisiae UtpB

SupramoleculeName: Saccharomyces cerevisiae UtpB / type: complex / ID: 1 / Parent: 0 / Details: Contains Utp1, Utp6, Utp12, Utp13, Utp18 and Utp21
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741
Molecular weightTheoretical: 525 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.7
Component:
ConcentrationNameFormula
50.0 mMHEPES-NaOH
300.0 mMsodium chlorideNaClSodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acid
StainingType: NEGATIVE / Material: 0.75% uranyl formate
GridModel: home-made carbon-coated copper grids / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 25.0 nm / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated defocus max: 1.6 µm / Calibrated defocus min: 1.6 µm / Calibrated magnification: 57555 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 25.0 e/Å2

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Image processing

Particle selectionNumber selected: 26510 / Details: tilt pairs manually selected
Startup modelType of model: RANDOM CONICAL TILT / Random conical tilt - Number images: 3836 / Random conical tilt - Tilt angle: 60 degrees
Initial angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 3836

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