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

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Basic information

Entry
Database: EMDB / ID: EMD-4113
Title30S-ABCE1 Post-Recycling Complex
Map data30S-ABCE1-Complex
Sample
  • Complex: 30S-ABCE1 complex
    • Complex: 30S subunits
    • Complex: ABCE1
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / oxidoreductase activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter-like, conserved site ...RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter ATP-binding protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
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 /
Abstract: Ribosome recycling orchestrated by the ATP binding cassette (ABC) protein ABCE1 can be considered as the final-or the first-step within the cyclic process of protein synthesis, connecting translation ...Ribosome recycling orchestrated by the ATP binding cassette (ABC) protein ABCE1 can be considered as the final-or the first-step within the cyclic process of protein synthesis, connecting translation termination and mRNA surveillance with re-initiation. An ATP-dependent tweezer-like motion of the nucleotide-binding domains in ABCE1 transfers mechanical energy to the ribosome and tears the ribosome subunits apart. The post-recycling complex (PRC) then re-initiates mRNA translation. Here, we probed the so far unknown architecture of the 1-MDa PRC (40S/30S·ABCE1) by chemical cross-linking and mass spectrometry (XL-MS). Our study reveals ABCE1 bound to the translational factor-binding (GTPase) site with multiple cross-link contacts of the helix-loop-helix motif to the S24e ribosomal protein. Cross-linking of the FeS cluster domain to the ribosomal protein S12 substantiates an extreme lever-arm movement of the FeS cluster domain during ribosome recycling. We were thus able to reconstitute and structurally analyse a key complex in the translational cycle, resembling the link between translation initiation and ribosome recycling.
History
DepositionSep 15, 2016-
Header (metadata) releaseOct 19, 2016-
Map releaseNov 23, 2016-
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: 0.000137
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.000137
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5lw7
  • Surface level: 0.000137
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5lw7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4113.png

Downloads & links

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Map

FileDownload / File: emd_4113.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation30S-ABCE1-Complex
Voxel sizeX=Y=Z: 1.062 Å
Density
Contour LevelBy AUTHOR: 0.000137 / Movie #1: 0.000137
Minimum - Maximum-0.00041378272 - 0.0023346527
Average (Standard dev.)0.000011249717 (±0.00016660261)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions480480480
Spacing480480480
CellA=B=C: 509.76 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: 30S-ABCE1 complex
    • Complex: 30S subunits
    • Complex: ABCE1

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Supramolecule #1: 30S-ABCE1 complex

SupramoleculeName: 30S-ABCE1 complex / type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 1.2 MDa

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Supramolecule #2: 30S subunits

SupramoleculeName: 30S subunits / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Sulfolobus solfataricus (archaea)

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Supramolecule #3: ABCE1

SupramoleculeName: ABCE1 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Sulfolobus solfataricus (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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
20.0 mMHEPES
100.0 mMPotassium acetateKOAc
1.0 mMMagnesium chlorideMgCl2
10.0 mMPotassium chlorideKCl
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 30S ribosomal subunits were reconstituted with purified, recombinantly expressed ABCE1

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: OTHER
Electron opticsCalibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 3.5 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Details: CTF correction was done following 3D reconstruction.
Startup modelType of model: OTHER / Details: Pyrococcus furiosus 30S ribosome
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 83
Software - Name: SPIDER (ver. 09.03)
Final 3D classificationSoftware - Name: SPIDER (ver. 09.03)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER (ver. 09.03)
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER (ver. 09.03) / Number images used: 19500

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-5lw7:
S. solfataricus ABCE1 post-splitting state

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