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- EMDB-1922: Ribosome Assembly Factors Prevent Premature Translation Initiatio... -

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Basic information

Entry
Database: EMDB / ID: EMD-1922
TitleRibosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates
Map dataImage of surface rendered view of Tsr1 recombinant protein
Sample
  • Sample: Recombinant Tsr1
  • Protein or peptide: Tsr1
Keywordspre-40S / Rio2-TAP / 40S intermediate
Function / homology
Function and homology information


endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribonucleoprotein complex binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GTPase activity / GTP binding ...endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribonucleoprotein complex binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GTPase activity / GTP binding / nucleolus / nucleus / cytoplasm
Similarity search - Function
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)
Similarity search - Domain/homology
Ribosome biogenesis protein TSR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 Å
AuthorsStrunk BS / Loucks CR / Su M / Vashisth H / Cheng S / Schilling J / BrooksIII CL / Karbstein K / Skiniotis G
CitationJournal: Science / Year: 2011
Title: Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates.
Authors: Bethany S Strunk / Cherisse R Loucks / Min Su / Harish Vashisth / Shanshan Cheng / Justin Schilling / Charles L Brooks / Katrin Karbstein / Georgios Skiniotis /
Abstract: Ribosome assembly in eukaryotes requires approximately 200 essential assembly factors (AFs) and occurs through ordered events that initiate in the nucleolus and culminate in the cytoplasm. Here, we ...Ribosome assembly in eukaryotes requires approximately 200 essential assembly factors (AFs) and occurs through ordered events that initiate in the nucleolus and culminate in the cytoplasm. Here, we present the electron cryo-microscopy (cryo-EM) structure of a late cytoplasmic 40S ribosome assembly intermediate from Saccharomyces cerevisiae at 18 angstrom resolution. We obtained cryo-EM reconstructions of preribosomal complexes lacking individual components to define the positions of all seven AFs bound to this intermediate. These late-binding AFs are positioned to prevent each step in the translation initiation pathway. Together, they obstruct the binding sites for initiation factors, prevent the opening of the messenger RNA channel, block 60S subunit joining, and disrupt the decoding site. These redundant mechanisms probably ensure that pre-40S particles do not enter the translation pathway, which would result in their rapid degradation.
History
DepositionJul 4, 2011-
Header (metadata) releaseNov 4, 2011-
Map releaseNov 4, 2011-
UpdateOct 1, 2014-
Current statusOct 1, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1922.png

Downloads & links

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Map

FileDownload / File: emd_1922.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationImage of surface rendered view of Tsr1 recombinant protein
Voxel sizeX=Y=Z: 4.16 Å
Density
Contour LevelBy EMDB: 0.35 / Movie #1: 0.35
Minimum - Maximum-0.191047 - 0.739237
Average (Standard dev.)-0.00581185 (±0.0573606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 266.24 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.164.164.16
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z266.240266.240266.240
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.1910.739-0.006

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Supplemental data

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Sample components

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Entire : Recombinant Tsr1

EntireName: Recombinant Tsr1
Components
  • Sample: Recombinant Tsr1
  • Protein or peptide: Tsr1

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Supramolecule #1000: Recombinant Tsr1

SupramoleculeName: Recombinant Tsr1 / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: 1 / Number unique components: 1
Molecular weightTheoretical: 91 KDa

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Macromolecule #1: Tsr1

MacromoleculeName: Tsr1 / type: protein_or_peptide / ID: 1 / Name.synonym: Tsr1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 91 KDa / Theoretical: 91 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Ribosome biogenesis protein TSR1

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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: 7.5 / Details: 50mM Tris-Cl 100mM NaCl 10mM MgCl2
StainingType: NEGATIVE / Details: See publication for details.
GridDetails: Continuous carbon grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 71138 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.1 µm
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER / Tilt angle max: 60
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 200 / Average electron dose: 20 e/Å2
Tilt angle min0

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Image processing

CTF correctionDetails: CTFTILT-FREALIGN
Final two d classificationNumber classes: 7
Final angle assignmentDetails: Realign convention
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider, frealign / Number images used: 3450
DetailsManual particle selection using WEB

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