+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4319 | |||||||||
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Title | uL23 beta hairpin loop deletion of E.coli ribosome | |||||||||
Map data | Sharpened map of E.coli ribosome with the beta-hairpin of uL23 deleted. | |||||||||
Sample |
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Keywords | uL23 / loop deletion / ribosomal tunnel / RIBOSOMAL PROTEIN | |||||||||
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 (E. coli) / Escherichia coli O157:H7 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Kudva R / von Heijne G | |||||||||
Funding support | Sweden, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4319.map.gz | 347.4 MB | EMDB map data format | |
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Header (meta data) | emd-4319-v30.xml emd-4319.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4319_fsc.xml | 19.1 KB | Display | FSC data file |
Images | emd_4319.png | 172.3 KB | ||
Masks | emd_4319_msk_1.map | 371.3 MB | Mask map | |
Filedesc metadata | emd-4319.cif.gz | 5.6 KB | ||
Others | emd_4319_half_map_1.map.gz emd_4319_half_map_2.map.gz | 344.3 MB 344.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4319 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4319 | HTTPS FTP |
-Validation report
Summary document | emd_4319_validation.pdf.gz | 459.3 KB | Display | EMDB validaton report |
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Full document | emd_4319_full_validation.pdf.gz | 458.4 KB | Display | |
Data in XML | emd_4319_validation.xml.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4319 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4319 | HTTPS FTP |
-Related structure data
Related structure data | 6fu8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4319.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map of E.coli ribosome with the beta-hairpin of uL23 deleted. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_4319_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map A of E.coli ribosome with the beta-hairpin of uL23 deleted.
File | emd_4319_half_map_1.map | ||||||||||||
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Annotation | Half map A of E.coli ribosome with the beta-hairpin of uL23 deleted. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of E.coli ribosome with the beta-hairpin of uL23 deleted.
File | emd_4319_half_map_2.map | ||||||||||||
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Annotation | Half map B of E.coli ribosome with the beta-hairpin of uL23 deleted. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E.coli ribosome with beta-hairpin of uL23 deleted
Entire | Name: E.coli ribosome with beta-hairpin of uL23 deleted |
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Components |
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-Supramolecule #1: E.coli ribosome with beta-hairpin of uL23 deleted
Supramolecule | Name: E.coli ribosome with beta-hairpin of uL23 deleted / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Deposited PDB is of the uL23 with the beta-hairpin loop deleted. |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 2.6 MDa |
-Macromolecule #1: 50S ribosomal protein L23
Macromolecule | Name: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli O157:H7 (bacteria) |
Molecular weight | Theoretical: 9.324003 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKRRSDWK KAYVTLKEGQ NL UniProtKB: Large ribosomal subunit protein uL23 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 0.02 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0003 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3500 / Average electron dose: 1.17 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6fu8: |