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- EMDB-3900: Polyproline stalled ribosome without EF-P -

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Basic information

Entry
Database: EMDB / ID: 3900
TitlePolyproline stalled ribosome without EF-P
SamplePolyproline stalled ribosome without EF-P.
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataPolyproline stalled ribosome without EF-P.
Methodsingle particle reconstruction, at 3.6 Å resolution
AuthorsHuter P / Arenz S / Wilson DW
CitationMol. Cell, 2017, 68, 515-527.e6

Mol. Cell, 2017, 68, 515-527.e6 Yorodumi Papers
Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.
Paul Huter / Stefan Arenz / Lars V Bock / Michael Graf / Jan Ole Frister / Andre Heuer / Lauri Peil / Agata L Starosta / Ingo Wohlgemuth / Frank Peske / Jiří Nováček / Otto Berninghausen / Helmut Grubmüller / Tanel Tenson / Roland Beckmann / Marina V Rodnina / Andrea C Vaiana / Daniel N Wilson

DateDeposition: Oct 5, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.195
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.195
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3900.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.06 Å/pix.
= 383.04 Å
360 pix
1.06 Å/pix.
= 383.04 Å
360 pix
1.06 Å/pix.
= 383.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.064 Å
Density
Contour Level:0.195 (by author), 0.195 (movie #1):
Minimum - Maximum-0.5373038 - 0.8077053
Average (Standard dev.)0.003607014 (0.034529816)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 383.04 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0641.0641.064
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z383.040383.040383.040
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.5370.8080.004

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Supplemental data

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Sample components

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Entire Polyproline stalled ribosome without EF-P.

EntireName: Polyproline stalled ribosome without EF-P. / Number of components: 1
MassTheoretical: 3 MDa

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Component #1: protein, Polyproline stalled ribosome without EF-P.

ProteinName: Polyproline stalled ribosome without EF-P. / Recombinant expression: No
MassTheoretical: 3 MDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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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: 28 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 53961
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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