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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
Map data
Sample40S-ABCE1 complex:
Function / homologyRibosomal protein S4/S9 / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S15P / Ribosomal protein S2, flavodoxin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S11, N-terminal / Ribosomal protein S5 domain 2-type fold ...Ribosomal protein S4/S9 / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S15P / Ribosomal protein S2, flavodoxin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S11, N-terminal / Ribosomal protein S5 domain 2-type fold / RLI, domain 1 / Ribosomal protein S8 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S17, conserved site / 4Fe-4S binding domain / Ribosomal protein S4, conserved site / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / ABC transporter, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Ribosomal S24e conserved site / Ribosomal protein S8e, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / ABC transporter / Ribosomal protein S12/S23 / Ribosomal protein S26e signature. / Ribosomal protein S12 signature. / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S17 signature. / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / ABC transporters family signature. / Ribosomal protein S15 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S6e signature. / Ribosomal protein S5 signature. / Ribosomal protein S30 / Ribosomal protein S5, C-terminal domain / Ribosomal protein S15 / Ribosomal family S4e / Ribosomal protein S2 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S17 / Ribosomal protein S8 / Ribosomal protein S11 / KOW motif / Ribosomal S3Ae family / Ribosomal protein S27 / Ribosomal protein S6e / Ribosomal protein S8e / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / Ribosomal protein S26e / S4 domain / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein S5, N-terminal / ATP-binding cassette, ABC transporter-type domain profile. / Ribosomal protein S15 / Ribosomal protein S7e / Ribosomal protein S17/S11 / Ribosomal protein S7e signature. / RLI1 / Ribosomal protein S2 signature 2. / Ribosomal protein S21e signature. / Ribosomal protein S27e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S8e signature. / S5 double stranded RNA-binding domain profile. / S4 RNA-binding domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Ribosomal protein S8 / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / SRP-dependent cotranslational protein targeting to membrane / RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsHeuer A / Gerovac M / Schmidt C / Trowitzsch S / Preis A / Koetter P / Berninghausen O / Becker T / 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
Validation ReportPDB-ID: 5ll6

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

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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
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5ll6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

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

Image control

Size
Brightness
Contrast
Others
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.

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
α=β=γ: 90 deg.

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
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 (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
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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