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- PDB-3j15: Model of ribosome-bound archaeal Pelota and ABCE1 -

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Basic information

Entry
Database: PDB / ID: 3j15
TitleModel of ribosome-bound archaeal Pelota and ABCE1
Components
  • ABC transporter ATP-binding protein
  • Protein pelota
KeywordsTRANSLATION/TRANSPORT PROTEIN / ribosome recycling / ribosome / archaea / TRANSLATION-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / ribosome binding / endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / cytoplasm
Similarity search - Function
Translation release factor pelota, archaea / Translation release factor pelota / Pelota/DOM34, N-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 ...Translation release factor pelota, archaea / Translation release factor pelota / Pelota/DOM34, N-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / Protein pelota homolog
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
Pyrococcus furiosus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsBecker, T. / Franckenberg, S. / Wickles, S. / Shoemaker, C.J. / Anger, A.M. / Armache, J.-P. / Sieber, H. / Ungewickell, C. / Berninghausen, O. / Daberkow, I. ...Becker, T. / Franckenberg, S. / Wickles, S. / Shoemaker, C.J. / Anger, A.M. / Armache, J.-P. / Sieber, H. / Ungewickell, C. / Berninghausen, O. / Daberkow, I. / Karcher, A. / Thomm, M. / Hopfner, K.-P. / Green, R. / Beckmann, R.
CitationJournal: Nature / Year: 2012
Title: Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.
Authors: Thomas Becker / Sibylle Franckenberg / Stephan Wickles / Christopher J Shoemaker / Andreas M Anger / Jean-Paul Armache / Heidemarie Sieber / Charlotte Ungewickell / Otto Berninghausen / Ingo ...Authors: Thomas Becker / Sibylle Franckenberg / Stephan Wickles / Christopher J Shoemaker / Andreas M Anger / Jean-Paul Armache / Heidemarie Sieber / Charlotte Ungewickell / Otto Berninghausen / Ingo Daberkow / Annette Karcher / Michael Thomm / Karl-Peter Hopfner / Rachel Green / Roland Beckmann /
Abstract: Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation ...Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined. In the eukaryotic and archaeal kingdoms, however, recycling involves the ABC-type ATPase ABCE1 and little is known about its structural basis. Here we present cryo-electron microscopy reconstructions of eukaryotic and archaeal ribosome recycling complexes containing ABCE1 and the termination factor paralogue Pelota. These structures reveal the overall binding mode of ABCE1 to be similar to canonical translation factors. Moreover, the iron-sulphur cluster domain of ABCE1 interacts with and stabilizes Pelota in a conformation that reaches towards the peptidyl transferase centre, thus explaining how ABCE1 may stimulate peptide-release activity of canonical termination factors. Using the mechanochemical properties of ABCE1, a conserved mechanism in archaea and eukaryotes is suggested that couples translation termination to recycling, and eventually to re-initiation.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Apr 18, 2012Group: Database references
Revision 1.4Jul 23, 2014Group: Other
Revision 1.5Sep 6, 2017Group: Data collection / Category: em_image_scans
Revision 1.6Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.7Aug 22, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / entity / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.src_method / _struct_ref.db_code ..._entity.src_method / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details

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Assembly

Deposited unit
A: Protein pelota
B: ABC transporter ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5186
Polymers107,9602
Non-polymers1,5584
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein pelota


Mass: 40673.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: pelA, TK0964 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3)
References: UniProt: Q5JIB9, Hydrolases; Acting on ester bonds
#2: Protein ABC transporter ATP-binding protein / ABCE1


Mass: 67286.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3)
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
Sequence detailsMODELED SEQUENCES WERE DERIVED FROM PYROCOCCUS KODAKARAENSIS (PELOTA) AND PYROCOCCUS ABYSSI (ABCE1). ...MODELED SEQUENCES WERE DERIVED FROM PYROCOCCUS KODAKARAENSIS (PELOTA) AND PYROCOCCUS ABYSSI (ABCE1). EXPERIMENTAL SOURCE ORGANISM WAS PYROCOCCUS FURIOSUS.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 70S ABCE1-Pelota complex / Type: RIBOSOME
Buffer solutionpH: 8.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 95 %
Details: Blot for 10 seconds before plunging into ethane (Vitrobot)
Method: Blot for 10 seconds before plunging, use 2 layer of filter paper

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Single particleSingle particle analysis / Resolution: 6.6 Å / Num. of particles: 51000 / Nominal pixel size: 1.2375 Å / Actual pixel size: 1.2375 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms7590 0 70 0 7660

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