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- EMDB-8766: Chateomium thermophilum Grc3/Las1 pre-rRNA Processing Machinery -

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Basic information

Entry
Database: EMDB / ID: EMD-8766
TitleChateomium thermophilum Grc3/Las1 pre-rRNA Processing Machinery
Map dataNone
Sample
  • Complex: Heterotetramer of Grc3 and Las1
Biological speciesChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsStanley RE / Pillon MC / Borgnia MJ
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Grc3 programs the essential endoribonuclease Las1 for specific RNA cleavage.
Authors: Monica C Pillon / Mack Sobhany / Mario J Borgnia / Jason G Williams / Robin E Stanley /
Abstract: Las1 is a recently discovered endoribonuclease that collaborates with Grc3-Rat1-Rai1 to process precursor ribosomal RNA (rRNA), yet its mechanism of action remains unknown. Disruption of the ...Las1 is a recently discovered endoribonuclease that collaborates with Grc3-Rat1-Rai1 to process precursor ribosomal RNA (rRNA), yet its mechanism of action remains unknown. Disruption of the mammalian Las1 gene has been linked to congenital lethal motor neuron disease and X-linked intellectual disability disorders, thus highlighting the necessity to understand Las1 regulation and function. Here, we report that the essential Las1 endoribonuclease requires its binding partner, the polynucleotide kinase Grc3, for specific C2 cleavage. Our results establish that Grc3 drives Las1 endoribonuclease cleavage to its targeted C2 site both in vitro and in Moreover, we observed Las1-dependent activation of the Grc3 kinase activity exclusively toward single-stranded RNA. Together, Las1 and Grc3 assemble into a tetrameric complex that is required for competent rRNA processing. The tetrameric Grc3/Las1 cross talk draws unexpected parallels to endoribonucleases RNaseL and Ire1, and establishes Grc3/Las1 as a unique member of the RNaseL/Ire1 RNA splicing family. Together, our work provides mechanistic insight for the regulation of the Las1 endoribonuclease and identifies the tetrameric Grc3/Las1 complex as a unique example of a protein-guided programmable endoribonuclease.
History
DepositionJun 14, 2017-
Header (metadata) releaseJun 28, 2017-
Map releaseJul 12, 2017-
UpdateJul 26, 2017-
Current statusJul 26, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.37
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4.37
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8766.png

Downloads & links

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Map

FileDownload / File: emd_8766.map.gz / Format: CCP4 / Size: 1 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.)
5.31 Å/pix.
x 64 pix.
= 339.84 Å		5.31 Å/pix.
x 64 pix.
= 339.84 Å		5.31 Å/pix.
x 64 pix.
= 339.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.37 / Movie #1: 4.37
Minimum - Maximum-2.2134933 - 10.668006999999999
Average (Standard dev.)0.092107415 (±0.74040425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 339.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.315.315.31
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z339.840339.840339.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-2.21310.6680.092

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Supplemental data

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Sample components

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Entire : Heterotetramer of Grc3 and Las1

EntireName: Heterotetramer of Grc3 and Las1
Components
  • Complex: Heterotetramer of Grc3 and Las1

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Supramolecule #1: Heterotetramer of Grc3 and Las1

SupramoleculeName: Heterotetramer of Grc3 and Las1 / type: complex / ID: 1 / Parent: 0
Details: Chaetomium thermophilum Grc3 lacking the protease-labile N-terminus bound to full-length Las1.
Source (natural)Organism: Chaetomium thermophilum (fungus)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: 8
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16442
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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