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- PDB-3izq: Structure of the Dom34-Hbs1-GDPNP complex bound to a translating ... -

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Basic information

Entry
Database: PDB / ID: 3izq
TitleStructure of the Dom34-Hbs1-GDPNP complex bound to a translating ribosome
Components
  • Elongation factor 1 alpha-like protein
  • Protein DOM34
KeywordsRIBOSOMAL PROTEIN / HYDROLASE / No-Go mRNA decay
Function / homology
Function and homology information


Eukaryotic Translation Elongation / RNA surveillance / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / ribosome disassembly / Protein methylation / nonfunctional rRNA decay / positive regulation of translational initiation ...Eukaryotic Translation Elongation / RNA surveillance / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / ribosome disassembly / Protein methylation / nonfunctional rRNA decay / positive regulation of translational initiation / translation elongation factor activity / Neutrophil degranulation / RNA endonuclease activity / rescue of stalled ribosome / positive regulation of translation / meiotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / cell division / GTPase activity / GTP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Translation release factor pelota / HBS1-like protein, N-terminal / Pelota/DOM34, N-terminal domain / HBS1 N-terminus / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 ...Translation release factor pelota / HBS1-like protein, N-terminal / Pelota/DOM34, N-terminal domain / HBS1 N-terminus / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / GTP-eEF1A C-terminal domain-like / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 50S ribosomal protein L30e-like / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Elongation factor 1 alpha-like protein / Protein DOM34
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsBecker, T. / Armache, J.-P. / Jarasch, A. / Anger, A.M. / Villa, E. / Sieber, H. / Abdel Motaal, B. / Mielke, T. / Berninghausen, O. / Beckmann, R.
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
Authors: Thomas Becker / Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Heidemarie Sieber / Basma Abdel Motaal / Thorsten Mielke / Otto Berninghausen / Roland Beckmann /
Abstract: No-go decay (NGD) is a mRNA quality-control mechanism in eukaryotic cells that leads to degradation of mRNAs stalled during translational elongation. The key factors triggering NGD are Dom34 and Hbs1. ...No-go decay (NGD) is a mRNA quality-control mechanism in eukaryotic cells that leads to degradation of mRNAs stalled during translational elongation. The key factors triggering NGD are Dom34 and Hbs1. We used cryo-EM to visualize NGD intermediates resulting from binding of the Dom34-Hbs1 complex to stalled ribosomes. At subnanometer resolution, all domains of Dom34 and Hbs1 were identified, allowing the docking of crystal structures and homology models. Moreover, the close structural similarity of Dom34 and Hbs1 to eukaryotic release factors (eRFs) enabled us to propose a model for the ribosome-bound eRF1-eRF3 complex. Collectively, our data provide structural insights into how stalled mRNA is recognized on the ribosome and how the eRF complex can simultaneously recognize stop codons and catalyze peptide release.
History
DepositionNov 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Assembly

Deposited unit
0: Protein DOM34
1: Elongation factor 1 alpha-like protein


Theoretical massNumber of molelcules
Total (without water)112,9462
Polymers112,9462
Non-polymers00
Water00
1


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

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Components

#1: Protein Protein DOM34 / Dom34p


Mass: 44119.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DOM34, N2016, YNL001W / Production host: Escherichia coli (E. coli)
References: UniProt: P33309, Hydrolases; Acting on ester bonds
#2: Protein Elongation factor 1 alpha-like protein / Hbs1p


Mass: 68826.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HBS1, YKR084C, YKR404 / Production host: Escherichia coli (E. coli) / References: UniProt: P32769

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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

Component
IDNameTypeParent-ID
1Ribosome-bound Dom34-Hbs1-GDPNP complexRIBOSOME0
2No-Go mRNA decay factor1
Buffer solutionpH: 7
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Carbon-coated Quantifoil with 2 nm carbon on top
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %
Details: Blotted for 10 seconds before plunging, used 2 layer of filter paper

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 39000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1300 nm / Cs: 2.26 mm
Specimen holderTemperature: 84 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 41
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1MDFFmodel fitting
2SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Single particle projection-matching / Resolution: 9.5 Å / Num. of particles: 38400 / Nominal pixel size: 1.2375 Å / Actual pixel size: 1.2375 Å / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms7183 0 0 0 7183

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