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- EMDB-6474: Cryo-EM structure of PoTC-EF-G(S588P)-GDPNP -

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Basic information

Entry
Database: EMDB / ID: EMD-6474
TitleCryo-EM structure of PoTC-EF-G(S588P)-GDPNP
Map dataReconstruction of PoTC-EF-G(S588P)-GDPNP
Sample
  • Sample: EF-G (S588P)-GDPNP bound to PoTC
  • Complex: PoTC 70S ribosome
Keywordsribosome recycling / PoTC / EF-G / RRF / cryo-EM
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsZhang D / Yan K / Zhang Y / Liu G / Cao X / Song G / Xie Q / Gao N / Qin Y
CitationJournal: Nucleic Acids Res / Year: 2015
Title: New insights into the enzymatic role of EF-G in ribosome recycling.
Authors: Dejiu Zhang / Kaige Yan / Yiwei Zhang / Guangqiao Liu / Xintao Cao / Guangtao Song / Qiang Xie / Ning Gao / Yan Qin /
Abstract: During translation, elongation factor G (EF-G) plays a catalytic role in tRNA translocation and a facilitative role in ribosome recycling. By stabilizing the rotated ribosome and interacting with ...During translation, elongation factor G (EF-G) plays a catalytic role in tRNA translocation and a facilitative role in ribosome recycling. By stabilizing the rotated ribosome and interacting with ribosome recycling factor (RRF), EF-G was hypothesized to induce the domain rotations of RRF, which subsequently performs the function of splitting the major intersubunit bridges and thus separates the ribosome into subunits for recycling. Here, with systematic mutagenesis, FRET analysis and cryo-EM single particle approach, we analyzed the interplay between EF-G/RRF and post termination complex (PoTC). Our data reveal that the two conserved loops (loop I and II) at the tip region of EF-G domain IV possess distinct roles in tRNA translocation and ribosome recycling. Specifically, loop II might be directly involved in disrupting the main intersubunit bridge B2a between helix 44 (h44 from the 30S subunit) and helix 69 (H69 from the 50S subunit) in PoTC. Therefore, our data suggest a new ribosome recycling mechanism which requires an active involvement of EF-G. In addition to supporting RRF, EF-G plays an enzymatic role in destabilizing B2a via its loop II.
History
DepositionSep 22, 2015-
Header (metadata) releaseOct 7, 2015-
Map releaseJun 8, 2016-
UpdateJun 8, 2016-
Current statusJun 8, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6474.tif

Downloads & links

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Map

FileDownload / File: emd_6474.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of PoTC-EF-G(S588P)-GDPNP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.06770778 - 0.13602762
Average (Standard dev.)0.00104923 (±0.00673398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0680.1360.001

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Supplemental data

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Sample components

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Entire : EF-G (S588P)-GDPNP bound to PoTC

EntireName: EF-G (S588P)-GDPNP bound to PoTC
Components
  • Sample: EF-G (S588P)-GDPNP bound to PoTC
  • Complex: PoTC 70S ribosome

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Supramolecule #1000: EF-G (S588P)-GDPNP bound to PoTC

SupramoleculeName: EF-G (S588P)-GDPNP bound to PoTC / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: PoTC 70S ribosome

SupramoleculeName: PoTC 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

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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

VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateAug 16, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: OTHER / Software - Name: Spider, RELION / Number images used: 17866
FSC plot (resolution estimation)

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