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- EMDB-4071: Structure of the 40S ABCE1 post-splitting complex in ribosome rec... -

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Basic information

Entry
Database: EMDB / ID: 4071
TitleStructure of the 40S ABCE1 post-splitting complex in ribosome recycling and translation initiation
Sample40S-ABCE1 complex
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map data
Methodsingle particle reconstruction, at 3.9 Å resolution
AuthorsHeuer A / Gerovac M / Schmidt C / Trowitzsch S / Preis A / Koetter P / Berninghausen O / Becker T / Beckmann R / Tampe R
CitationNat. Struct. Mol. Biol., 2017, 24, 453-460

Nat. Struct. Mol. Biol., 2017, 24, 453-460 StrPapers
Structure of the 40S-ABCE1 post-splitting complex in ribosome recycling and translation initiation.
André Heuer / Milan Gerovac / Christian Schmidt / Simon Trowitzsch / Anne Preis / Peter Kötter / Otto Berninghausen / Thomas Becker / Roland Beckmann / Robert Tampé

DateDeposition: Jul 26, 2016 / Header (metadata) release: Oct 12, 2016 / Map release: Apr 5, 2017 / Last update: Jul 26, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5ll6
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_4071.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.08 Å/pix.
= 416.256 Å
384 pix
1.08 Å/pix.
= 416.256 Å
384 pix
1.08 Å/pix.
= 416.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour Level:0.038 (by emdb), 0.045 (movie #1):
Minimum - Maximum-0.19473614 - 0.47236273
Average (Standard dev.)0.0003276198 (0.012925588)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 416.25598 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1950.4720.000

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Supplemental data

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Sample components

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Entire 40S-ABCE1 complex

EntireName: 40S-ABCE1 complex / Number of components: 1
MassTheoretical: 1.2 MDa

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Component #1: protein, 40S-ABCE1 complex

ProteinName: 40S-ABCE1 complex / Recombinant expression: No
MassTheoretical: 1.2 MDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.4 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: - 2400 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 102000
3D reconstructionSoftware: RELION / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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