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- EMDB-3452: native 40S-ABCE1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3452
Titlenative 40S-ABCE1 complex
Map datanative 40s ABCE1 complex
Sample
  • Complex: native 40S-ABCE1 complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsHeuer A / Beckmann R / Tampe R
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Structure of the 40S-ABCE1 post-splitting complex in ribosome recycling and translation initiation.
Authors: André Heuer / Milan Gerovac / Christian Schmidt / Simon Trowitzsch / Anne Preis / Peter Kötter / Otto Berninghausen / Thomas Becker / Roland Beckmann / Robert Tampé /
Abstract: The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the ...The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the underlying splitting mechanism remains enigmatic. Here, we present a cryo-EM structure of the yeast 40S-ABCE1 post-splitting complex at 3.9-Å resolution. Compared to the pre-splitting state, we observe repositioning of ABCE1's iron-sulfur cluster domain, which rotates 150° into a binding pocket on the 40S subunit. This repositioning explains a newly observed anti-association activity of ABCE1. Notably, the movement implies a collision with A-site factors, thus explaining the splitting mechanism. Disruption of key interactions in the post-splitting complex impairs cellular homeostasis. Additionally, the structure of a native post-splitting complex reveals ABCE1 to be part of the 43S initiation complex, suggesting a coordination of termination, recycling, and initiation.
History
DepositionNov 1, 2016-
Header (metadata) releaseDec 7, 2016-
Map releaseApr 19, 2017-
UpdateJul 26, 2017-
Current statusJul 26, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00465
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.00465
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3452.png

Downloads & links

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Map

FileDownload / File: emd_3452.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnative 40s ABCE1 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 416.256 Å		1.08 Å/pix.
x 384 pix.
= 416.256 Å		1.08 Å/pix.
x 384 pix.
= 416.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00465 / Movie #1: 0.00465
Minimum - Maximum-0.010372743 - 0.033858944
Average (Standard dev.)0.00013775792 (±0.002919868)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 416.25598 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z416.256416.256416.256
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0100.0340.000

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Supplemental data

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Sample components

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Entire : native 40S-ABCE1 complex

EntireName: native 40S-ABCE1 complex
Components
  • Complex: native 40S-ABCE1 complex

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Supramolecule #1: native 40S-ABCE1 complex

SupramoleculeName: native 40S-ABCE1 complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.2 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMTris
50.0 mMPotassium acetateKOAc
15.0 mMMagnesium acetateMgOAc
1.0 mMDithiothreitolDTT
GridModel: Quantifoil R3/3 / Material: COPPER/PALLADIUM / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified 40S ribosomal subunits were reconstituted with purified, recombinantly expressed ABCE1

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 4)
Details: CTF correction was done following 3D reconstruction.
Startup modelType of model: OTHER / Details: yeast 40S ribosome
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 2), SPIDER) / Number images used: 9500
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2)
Final 3D classificationSoftware - Name: RELION (ver. 2)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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