+Open data
-Basic information
Entry | Database: PDB / ID: 6fu8 | ||||||
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Title | uL23 beta hairpin loop deletion of E.coli ribosome | ||||||
Components | 50S ribosomal protein L23 | ||||||
Keywords | RIBOSOMAL PROTEIN / uL23 / loop deletion / ribosomal tunnel | ||||||
Function / homology | Function and homology information ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Kudva, R. / von Heijne, G. / Carroni, M. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6fu8.cif.gz | 39.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fu8.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fu8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6fu8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6fu8_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 6fu8_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/6fu8 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/6fu8 | HTTPS FTP |
-Related structure data
Related structure data | 4319MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 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 |
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Molecular weight | Value: 2.6 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron 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 scans | Movie frames/image: 20 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 471272 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 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 building | Protocol: RIGID BODY FIT |