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- PDB-3jbs: eL6 protein from yeast 60S ribosomal subunit -

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Basic information

Entry
Database: PDB / ID: 3jbs
TitleeL6 protein from yeast 60S ribosomal subunit
ComponentseL6
KeywordsTRANSLATION / ribosome
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome ...SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / RNA binding / cytosol
Similarity search - Function
: / Ribosomal protein L6e signature. / Ribosomal Protein L6, KOW domain / Ribosomal protein L6e / 60S ribosomal protein L6E / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
Large ribosomal subunit protein eL6A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPassos, D.O. / Lyumkis, D.
CitationJournal: J Struct Biol / Year: 2015
Title: Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits.
Authors: Dario Oliveira Passos / Dmitry Lyumkis /
Abstract: A single-particle cryoEM reconstruction of the large ribosomal subunit from Saccharomyces cerevisiae was obtained from a dataset of ∼75,000 particles. The gold-standard and frequency-limited ...A single-particle cryoEM reconstruction of the large ribosomal subunit from Saccharomyces cerevisiae was obtained from a dataset of ∼75,000 particles. The gold-standard and frequency-limited approaches to single-particle refinement were each independently used to determine orientation parameters for the final reconstruction. Both approaches showed similar resolution curves and nominal resolution values for the 60S dataset, estimated at 2.9 Å. The amount of over-fitting present during frequency-limited refinement was quantitatively analyzed using the high-resolution phase-randomization test, and the results showed no apparent over-fitting. The number of asymmetric subunits required to reach specific resolutions was subsequently analyzed by refining subsets of the data in an ab initio manner. With our data collection and processing strategies, sub-nanometer resolution was obtained with ∼200 asymmetric subunits (or, equivalently for the ribosomal subunit, particles). Resolutions of 5.6 Å, 4.5 Å, and 3.8 Å were reached with ∼1000, ∼1600, and ∼5000 asymmetric subunits, respectively. At these resolutions, one would expect to detect alpha-helical pitch, separation of beta-strands, and separation of Cα atoms, respectively. Using this map, together with strategies for ab initio model building and model refinement, we built a region of the ribosomal protein eL6, which was missing in previous models of the yeast ribosome. The relevance for more routine high-resolution structure determination is discussed.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: eL6


Theoretical massNumber of molelcules
Total (without water)20,0011
Polymers20,0011
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 eL6 / L17 / RP18 / YL16 / 60S ribosomal protein L6-A


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cytosolic extract / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q02326

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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: Saccharomyces cerevisiae large 60S ribosomal subunit / Type: RIBOSOME
Molecular weightValue: 2.5 MDa / Experimental value: NO
Buffer solutionName: elution buffer (50 mM HEPES-KOH, 100 mM KOAc, 5 mM MgOAc, 1 mM EDTA, 2 mM DTT)
pH: 6.8
Details: elution buffer (50 mM HEPES-KOH, 100 mM KOAc, 5 mM MgOAc, 1 mM EDTA, 2 mM DTT)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh, 1.2x1.3 micron C-flat grids, plasma-treated for 5 seconds
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 77 K / Humidity: 90 %
Details: A 3 uL sample was applied onto a freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb for 30 seconds. ...Details: A 3 uL sample was applied onto a freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb for 30 seconds. The sample was then plunge-frozen in liquid ethane using a manual cryo-plunger in ambient atmosphere at 4 degrees C.
Method: A 3 uL sample was applied onto a freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb for 30 seconds. ...Method: A 3 uL sample was applied onto a freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb for 30 seconds. The sample was then plunge-frozen in liquid ethane using a manual cryo-plunger in ambient atmosphere at 4 degrees C.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Sep 2, 2014 / Details: super-resolution imaging
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 38167 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Astigmatism: Objective lens astigmatism was corrected within the Leginon software.
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 1833

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Processing

EM software
IDNameCategory
1Rosettamodel fitting
2UCSF Chimeramodel fitting
3FREALIGN3D reconstruction
CTF correctionDetails: each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: projection matching / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75653 / Nominal pixel size: 1.31 Å / Actual pixel size: 1.31 Å
Details: B-factor of -50 applied to final map (Single particle--Applied symmetry: C1).
Symmetry type: POINT
Atomic model buildingB value: 50 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: FSC / Details: REFINEMENT PROTOCOL--flexible
Atomic model buildingPDB-ID: 4UJQ

4ujq
PDB Unreleased entry


Pdb chain-ID: H / Accession code: 4UJQ / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 0 0 1401

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