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- EMDB-4319: uL23 beta hairpin loop deletion of E.coli ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-4319
TitleuL23 beta hairpin loop deletion of E.coli ribosome
Map dataSharpened map of E.coli ribosome with the beta-hairpin of uL23 deleted.
Sample
  • Complex: E.coli ribosome with beta-hairpin of uL23 deleted
    • Protein or peptide: 50S ribosomal protein L23
KeywordsuL23 / 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 / ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli O157:H7 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKudva R / von Heijne G
Funding support Sweden, 1 items
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, 2018-
Header (metadata) releaseMar 14, 2018-
Map releaseDec 5, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.536
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.536
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6fu8
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6fu8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4319.png

Downloads & links

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Map

FileDownload / File: emd_4319.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of E.coli ribosome with the beta-hairpin of uL23 deleted.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 460 pix.
= 501.4 Å		1.09 Å/pix.
x 460 pix.
= 501.4 Å		1.09 Å/pix.
x 460 pix.
= 501.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.536 / Movie #1: 0.536
Minimum - Maximum-0.5661596 - 1.9835955
Average (Standard dev.)-0.009908884 (±0.12531587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 501.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z501.400501.400501.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-0.5661.984-0.010

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Supplemental data

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Mask #1

Fileemd_4319_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of E.coli ribosome with the beta-hairpin of uL23 deleted.

Fileemd_4319_half_map_1.map
AnnotationHalf map A of E.coli ribosome with the beta-hairpin of uL23 deleted.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of E.coli ribosome with the beta-hairpin of uL23 deleted.

Fileemd_4319_half_map_2.map
AnnotationHalf map B of E.coli ribosome with the beta-hairpin of uL23 deleted.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E.coli ribosome with beta-hairpin of uL23 deleted

EntireName: E.coli ribosome with beta-hairpin of uL23 deleted
Components
  • Complex: E.coli ribosome with beta-hairpin of uL23 deleted
    • Protein or peptide: 50S ribosomal protein L23

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Supramolecule #1: E.coli ribosome with beta-hairpin of uL23 deleted

SupramoleculeName: 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.
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 2.6 MDa

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Macromolecule #1: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O157:H7 (bacteria)
Molecular weightTheoretical: 9.324003 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKRRSDWK KAYVTLKEGQ NL

UniProtKB: Large ribosomal subunit protein uL23

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridMaterial: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 471272
Startup modelType of model: NONE / Details: Ab initio done using cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: All processing from ab initio to refinement and sharpening performed in cryosparc
Number images used: 132029
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

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

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