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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: 4319
TitleuL23 beta hairpin loop deletion of E.coli ribosome
Map dataSharpened map of E.coli ribosome with the beta-hairpin of uL23 deleted.
SampleE.coli ribosome with beta-hairpin of uL23 deleted:
50S ribosomal protein L23
Function / homologyRibosomal protein L23/L25, conserved site / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L25/L23 / Ribosomal protein L23 / Ribosomal protein L23 signature. / ribosome / rRNA binding / structural constituent of ribosome / translation / 50S ribosomal protein L23
Function and homology information
SourceEscherichia coli (E. coli) / Escherichia coli O157:H7 (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsKudva R / von Heijne G / Carroni M
CitationJournal: Elife / Year: 2018
Title: The shape of the ribosome exit tunnel affects cotranslational protein folding.
Authors: Renuka Kudva / Pengfei Tian / Fátima Pardo-Avila / Marta Carroni / Robert Best / Harris D Bernstein / Gunnar von Heijne
Validation ReportPDB-ID: 6fu8

SummaryFull reportAbout validation report
DateDeposition: Feb 26, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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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 models: PDB-6fu8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4319.map.gz (map file in CCP4 format, 389345 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
460 pix
1.09 Å/pix.
= 501.4 Å
460 pix
1.09 Å/pix.
= 501.4 Å
460 pix
1.09 Å/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
Contour Level:0.536 (by author), 0.536 (movie #1):
Minimum - Maximum-0.5661596 - 1.9835955
Average (Standard dev.)-0.009908884 (0.12531587)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions460460460
Origin0.00.00.0
Limit459.0459.0459.0
Spacing460460460
CellA=B=C: 501.40002 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ000
NX/NY/NZ450450450
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

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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
Details: Deposited PDB is of the uL23 with the beta-hairpin loop deleted.
Number of components: 2

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Component #1: protein, E.coli ribosome with beta-hairpin of uL23 deleted

ProteinName: E.coli ribosome with beta-hairpin of uL23 deleted
Details: Deposited PDB is of the uL23 with the beta-hairpin loop deleted.
Recombinant expression: No
MassTheoretical: 2.6 MDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.324003 kDa
SourceSpecies: Escherichia coli O157:H7 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.17 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3500

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 132029
3D reconstructionAlgorithm: BACK PROJECTION / Software: cryoSPARC / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
Details: All processing from ab initio to refinement and sharpening performed in cryosparc
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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