+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4113 | |||||||||
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Title | 30S-ABCE1 Post-Recycling Complex | |||||||||
Map data | 30S-ABCE1-Complex | |||||||||
Sample |
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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 | |||||||||
Biological species | Sulfolobus solfataricus (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.0 Å | |||||||||
Authors | Heuer A / Beckmann R / Tampe R | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4113.map.gz | 352 MB | EMDB map data format | |
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Header (meta data) | emd-4113-v30.xml emd-4113.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_4113.png | 212.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4113 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4113 | HTTPS FTP |
-Validation report
Summary document | emd_4113_validation.pdf.gz | 194.4 KB | Display | EMDB validaton report |
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Full document | emd_4113_full_validation.pdf.gz | 193.5 KB | Display | |
Data in XML | emd_4113_validation.xml.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4113 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4113 | HTTPS FTP |
-Related structure data
Related structure data | 5lw7MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4113.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 30S-ABCE1-Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.062 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 30S-ABCE1 complex
Entire | Name: 30S-ABCE1 complex |
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Components |
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-Supramolecule #1: 30S-ABCE1 complex
Supramolecule | Name: 30S-ABCE1 complex / type: complex / ID: 1 / Parent: 0 |
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Molecular weight | Theoretical: 1.2 MDa |
-Supramolecule #2: 30S subunits
Supramolecule | Name: 30S subunits / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Sulfolobus solfataricus (archaea) |
-Supramolecule #3: ABCE1
Supramolecule | Name: ABCE1 / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Sulfolobus solfataricus (archaea) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: 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 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Purified 30S ribosomal subunits were reconstituted with purified, recombinantly expressed ABCE1 |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: OTHER |
Electron optics | Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 3.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-5lw7: |