Journal: 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
Deposition
Oct 17, 2016
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Header (metadata) release
Oct 26, 2016
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Map release
Dec 21, 2016
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Update
Sep 20, 2017
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Current status
Sep 20, 2017
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_4153.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Partial Elp123 sub-complex from S.cerevisiae in which one of the Elp2 subunits is missing.
Voxel size
X=Y=Z: 2.2 Å
Density
Contour Level
By AUTHOR: 0.0284 / Movie #1: 0.0284
Minimum - Maximum
-0.043942522 - 0.10950313
Average (Standard dev.)
0.000026676707 (±0.005108263)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
224
224
224
Spacing
224
224
224
Cell
A=B=C: 492.80002 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.2
2.2
2.2
M x/y/z
224
224
224
origin x/y/z
0.000
0.000
0.000
length x/y/z
492.800
492.800
492.800
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
224
224
224
D min/max/mean
-0.044
0.110
0.000
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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 ...
Entire
Name: 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 ...
Supramolecule
Name: 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.
Type: 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)
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