+Open data
-Basic information
Entry | Database: PDB / ID: 5lw7 | ||||||
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Title | S. solfataricus ABCE1 post-splitting state | ||||||
Components | ABC transporter ATP-binding protein | ||||||
Keywords | RIBOSOME / ABCE1 / recycling / 30S | ||||||
Function / homology | Function and homology information ribosomal small subunit binding / translational termination / translational initiation / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17 Å | ||||||
Authors | Heuer, A. / Gerovac, M. / Beckmann, R. / Tampe, R. | ||||||
Funding support | Germany, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5lw7.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lw7.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 5lw7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lw7_validation.pdf.gz | 663.8 KB | Display | wwPDB validaton report |
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Full document | 5lw7_full_validation.pdf.gz | 690.8 KB | Display | |
Data in XML | 5lw7_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 5lw7_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/5lw7 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/5lw7 | HTTPS FTP |
-Related structure data
Related structure data | 4113MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 67286.273 Da / Num. of mol.: 1 / Mutation: E238A E485A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea) Gene: PAB0824 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UZA4 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: S. solfataricus ABCE1 post-splitting state / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES | |||||||||||||||||||||||||
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Molecular weight | Value: 0.067 MDa / Experimental value: NO | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER/PALLADIUM / Grid type: Quantifoil R3/3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI SPIRIT |
Electron gun | Electron source: OTHER / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 35000 nm / Calibrated defocus min: 10000 nm / Cs: 2.2 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 17 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 19500 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |