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- EMDB-4113: 30S-ABCE1 Post-Recycling Complex -

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Basic information

Entry
Database: EMDB / ID: 4113
Title30S-ABCE1 Post-Recycling Complex
Map data30S-ABCE1-Complex
Sample30S-ABCE1 complex:
30S subunits / ABCE1
Function / homology4Fe-4S ferredoxin, iron-sulphur binding, conserved site / ATP-binding cassette, ABC transporter-type domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S binding domain / ABC transporter / RLI, domain 1 / P-loop containing nucleoside triphosphate hydrolase / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter, conserved site ...4Fe-4S ferredoxin, iron-sulphur binding, conserved site / ATP-binding cassette, ABC transporter-type domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S binding domain / ABC transporter / RLI, domain 1 / P-loop containing nucleoside triphosphate hydrolase / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter, conserved site / RLI1 / RNase L inhibitor RLI, possible metal-binding domain / AAA+ ATPase domain / ABC transporter-like / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / ABC transporters family signature. / 4 iron, 4 sulfur cluster binding / ATPase activity / ATP binding / metal ion binding / ABC transporter ATP-binding protein
Function and homology information
SourceSulfolobus solfataricus (acidophilic)
Methodsingle particle reconstruction / cryo EM / 17 Å resolution
AuthorsHeuer A / Beckmann R / Tampe R
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry.
Authors: Kristin Kiosze-Becker / Alessandro Ori / Milan Gerovac / André Heuer / Elina Nürenberg-Goloub / Umar Jan Rashid / Thomas Becker / Roland Beckmann / Martin Beck / Robert Tampé
Validation ReportPDB-ID: 5lw7

SummaryFull reportAbout validation report
DateDeposition: Sep 15, 2016 / Header (metadata) release: Oct 19, 2016 / Map release: Nov 23, 2016 / Last update: Jul 26, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.000137
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.000137
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5lw7
  • Surface level: 0.000137
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5lw7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4113.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
1.06 Å/pix.
= 509.76 Å
480 pix
1.06 Å/pix.
= 509.76 Å
480 pix
1.06 Å/pix.
= 509.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.062 Å
Density
Contour Level:0.000137 (by author), 0.000137 (movie #1):
Minimum - Maximum-0.00041378272 - 0.0023346527
Average (Standard dev.)1.1249717E-5 (0.00016660261)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin-50-50-50
Limit429429429
Spacing480480480
CellA=B=C: 509.76 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0621.0621.062
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z509.760509.760509.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS480480480
D min/max/mean-0.0000.0020.000

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Supplemental data

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Sample components

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Entire 30S-ABCE1 complex

EntireName: 30S-ABCE1 complex / Number of components: 3
MassTheoretical: 1.2 MDa

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Component #1: protein, 30S-ABCE1 complex

ProteinName: 30S-ABCE1 complex / Recombinant expression: No
MassTheoretical: 1.2 MDa

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Component #2: protein, 30S subunits

ProteinName: 30S subunits / Recombinant expression: No
SourceSpecies: Sulfolobus solfataricus (acidophilic)

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Component #3: protein, ABCE1

ProteinName: ABCE1 / Recombinant expression: No
SourceSpecies: Sulfolobus solfataricus (acidophilic)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: OTHER / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: - 3500 nm
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F816 (8k x 8k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 19500
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER
CTF correction: CTF correction was done following 3D reconstruction.
Resolution: 17 Å / Resolution method: FSC 0.5 CUT-OFF

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Atomic model buiding

Output model

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