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- EMDB-4153: S.cerevisiae partial Elp123 sub-complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4153
TitleS.cerevisiae partial Elp123 sub-complex
Map dataPartial Elp123 sub-complex from S.cerevisiae in which one of the Elp2 subunits is missing.
Sample
  • Complex: S.cerevisiae partial Elp123 sub-complex, without one of the Elp2 subunits.
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 31.0 Å
AuthorsDauden MI / Kosinski J / Kolaj-Robin O / Desfosses A / Ori A / Faux C / Hoffmann NA / Onuma OF / Breuring KD / Beck M ...Dauden MI / Kosinski J / Kolaj-Robin O / Desfosses A / Ori A / Faux C / Hoffmann NA / Onuma OF / Breuring KD / Beck M / Sachse C / Seraphin B / Glatt S / Mueller CW
CitationJournal: EMBO Rep / Year: 2017
Title: Architecture of the yeast Elongator complex.
Authors: Maria I Dauden / Jan Kosinski / Olga Kolaj-Robin / Ambroise Desfosses / Alessandro Ori / Celine Faux / Niklas A Hoffmann / Osita F Onuma / Karin D Breunig / Martin Beck / Carsten Sachse / ...Authors: Maria I Dauden / Jan Kosinski / Olga Kolaj-Robin / Ambroise Desfosses / Alessandro Ori / Celine Faux / Niklas A Hoffmann / Osita F Onuma / Karin D Breunig / Martin Beck / Carsten Sachse / Bertrand Séraphin / Sebastian Glatt / Christoph W Müller /
Abstract: The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is ...The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is formed by six individual subunits (Elp1-6) that are all equally important for its tRNA modification activity. However, its overall architecture and the detailed reaction mechanism remain elusive. Here, we report the structures of the fully assembled yeast Elongator and the Elp123 sub-complex solved by an integrative structure determination approach showing that two copies of the Elp1, Elp2, and Elp3 subunits form a two-lobed scaffold, which binds Elp456 asymmetrically. Our topological models are consistent with previous studies on individual subunits and further validated by complementary biochemical analyses. Our study provides a structural framework on how the tRNA modification activity is carried out by Elongator.
History
DepositionOct 17, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseDec 21, 2016-
UpdateSep 20, 2017-
Current statusSep 20, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0284
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0284
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4153.png

Downloads & links

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Map

FileDownload / File: emd_4153.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPartial Elp123 sub-complex from S.cerevisiae in which one of the Elp2 subunits is missing.
Voxel sizeX=Y=Z: 2.2 Å
Density
Contour LevelBy AUTHOR: 0.0284 / Movie #1: 0.0284
Minimum - Maximum-0.043942522 - 0.10950313
Average (Standard dev.)0.000026676707 (±0.005108263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 492.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z492.800492.800492.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0440.1100.000

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Supplemental data

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Sample components

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Entire : S.cerevisiae partial Elp123 sub-complex, without one of the Elp2 ...

EntireName: S.cerevisiae partial Elp123 sub-complex, without one of the Elp2 subunits.
Components
  • Complex: S.cerevisiae partial Elp123 sub-complex, without one of the Elp2 subunits.

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Supramolecule #1: S.cerevisiae partial Elp123 sub-complex, without one of the Elp2 ...

SupramoleculeName: S.cerevisiae partial Elp123 sub-complex, without one of the Elp2 subunits.
type: complex / ID: 1 / Parent: 0
Details: Composed of two copies of Elp1 and Elp3 and only one copy of Elp2.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BS1173
Molecular weightTheoretical: 530 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

Concentration0.035 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES buffer
125.0 mMNaClSodium chlorideSodium chloride
5.0 mMC2H6OS2-mercaptoethanol
StainingType: NEGATIVE / Material: Uranyl Acetate
Details: 3.5 ul aliquots of freshly purified Elp123 complex were applied to glow discharged carbon copper-collodion (Sigma) grids for 2 min and stained with a 1% uranyl acetate solution (w/v)
GridModel: Plano D-35578 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Details: 0.45mBar, 20mA

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 6.3 mm / Nominal magnification: 49000
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 1 / Number real images: 216 / Average electron dose: 16.0 e/Å2

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Image processing

Particle selectionNumber selected: 50034
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: RANDOM CONICAL TILT / Random conical tilt - Number images: 120 / Random conical tilt - Tilt angle: 55 degrees
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: Xmipp
Final 3D classificationNumber classes: 2 / Avg.num./class: 3200 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 31.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 1946

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