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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 / homologyeRF1 domain 1/Pelota-like / eRF1 domain 1 / Elongation factor Tu GTP binding domain / Pelota/DOM34, N-terminal domain / Tr-type G domain, conserved site / 50S ribosomal protein L30e-like / P-loop containing nucleoside triphosphate hydrolase / HBS1-like protein, N-terminal / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation protein, beta-barrel domain superfamily ...eRF1 domain 1/Pelota-like / eRF1 domain 1 / Elongation factor Tu GTP binding domain / Pelota/DOM34, N-terminal domain / Tr-type G domain, conserved site / 50S ribosomal protein L30e-like / P-loop containing nucleoside triphosphate hydrolase / HBS1-like protein, N-terminal / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation protein, beta-barrel domain superfamily / eRF1 domain 3 / eRF1 domain 2 / Translation release factor pelota / Translation elongation factor EFTu/EF1A, C-terminal / Transcription factor, GTP-binding domain / Elongation factor Tu C-terminal domain / eRF1 domain 2 / eRF1 domain 3 / HBS1 N-terminus / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / ribosome disassembly / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / translation elongation factor activity / endoribonuclease activity / positive regulation of translation / meiotic cell cycle / translation / Acting on Ester Bonds / GTPase activity / cell division / GTP binding / metal ion binding / cytoplasm / Elongation factor 1 alpha-like protein / Protein DOM34
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9.5 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 30, 2010 / Release: Jun 1, 2011
RevisionDateData content typeGroupProviderType
1.0Jun 1, 2011Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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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
Polyers112,9462
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide Protein DOM34 / Dom34p


Mass: 44119.797 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: DOM34, N2016, YNL001W / Production host: Escherichia coli (E. coli) / References: UniProt: P33309, Acting on Ester Bonds
#2: Protein/peptide Elongation factor 1 alpha-like protein / Hbs1p


Mass: 68826.406 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker'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 / 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
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 / Calibrated magnification: 39000 / Nominal defocus max: 4000 nm / Nominal defocus min: 1300 nm / Cs: 2.26 mm
Specimen holderTemperature: 84 kelvins
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 41
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m 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
3D reconstructionMethod: Single particle projection-matching / Resolution: 9.5 Å / Number of particles: 38400 / Nominal pixel size: 1.2375 / Actual pixel size: 1.2375 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Number of atoms included #LASTProtein: 7183 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7183

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