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- PDB-6fu8: uL23 beta hairpin loop deletion of E.coli ribosome -

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Basic information

Entry
Database: PDB / ID: 6fu8
TitleuL23 beta hairpin loop deletion of E.coli ribosome
Components50S ribosomal protein L23
KeywordsRIBOSOMAL PROTEIN / uL23 / loop deletion / ribosomal tunnel
Function / homology
Function and homology information


ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm
Similarity search - Function
RRM (RNA recognition motif) domain / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L25/L23 / Ribosomal protein L23 / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKudva, R. / von Heijne, G. / Carroni, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Elife / Year: 2018
Title: The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding.
Authors: Renuka Kudva / Pengfei Tian / Fátima Pardo-Avila / Marta Carroni / Robert B Best / Harris D Bernstein / Gunnar von Heijne /
Abstract: The ribosome exit tunnel can accommodate small folded proteins, while larger ones fold outside. It remains unclear, however, to what extent the geometry of the tunnel influences protein folding. ...The ribosome exit tunnel can accommodate small folded proteins, while larger ones fold outside. It remains unclear, however, to what extent the geometry of the tunnel influences protein folding. Here, using ribosomes with deletions in loops in proteins uL23 and uL24 that protrude into the tunnel, we investigate how tunnel geometry determines where proteins of different sizes fold. We find that a 29-residue zinc-finger domain normally folding close to the uL23 loop folds deeper in the tunnel in uL23 Δloop ribosomes, while two ~ 100 residue proteins normally folding close to the uL24 loop near the tunnel exit port fold at deeper locations in uL24 Δloop ribosomes, in good agreement with results obtained by coarse-grained molecular dynamics simulations. This supports the idea that cotranslational folding commences once a protein domain reaches a location in the exit tunnel where there is sufficient space to house the folded structure.
History
DepositionFeb 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
C: 50S ribosomal protein L23


Theoretical massNumber of molelcules
Total (without water)9,3241
Polymers9,3241
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NA
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5880 Å2
MethodPISA

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Components

#1: Protein 50S ribosomal protein L23 /


Mass: 9324.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: rplW, Z4689, ECs4183 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ2, UniProt: P0ADZ0*PLUS

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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: E.coli ribosome with beta-hairpin of uL23 deleted / Type: RIBOSOME
Details: Deposited PDB is of the uL23 with the beta-hairpin loop deleted.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 2.6 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.17 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3500
Image scansMovie frames/image: 20

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Processing

EM software
IDNameVersionCategory
2EPU1.09image acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
12cryoSPARC3D reconstruction
13Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 471272
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132029 / Algorithm: BACK PROJECTION
Details: All processing from ab initio to refinement and sharpening performed in cryosparc
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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