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- EMDB-1127: Mechanism for the disassembly of the posttermination complex infe... -

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Basic information

Entry
Database: EMDB / ID: EMD-1127
TitleMechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Map dataThis is a 50S.EF-G.GDPNP.RRF complex from E.coli
Sample
  • Sample: 50S.EF-G.GDPNP.RRF complex from E.coli
  • Complex: 50S subunitProkaryotic large ribosomal subunit
  • Protein or peptide: RRF
  • Protein or peptide: EF-G
Function / homology
Function and homology information


cytoplasmic translational termination / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding ...cytoplasmic translational termination / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / cytosol / cytoplasm
Similarity search - Function
Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein S12, bacterial-type / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S12 signature. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein uS12 / Ribosome-recycling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 15.5 Å
AuthorsGao N / Zavialov AV / Li W / Sengupta J / Valle M / Gursky RP / Ehrenberg M / Frank J
CitationJournal: Mol Cell / Year: 2005
Title: Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Authors: Ning Gao / Andrey V Zavialov / Wen Li / Jayati Sengupta / Mikel Valle / Richard P Gursky / Måns Ehrenberg / Joachim Frank /
Abstract: Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In ...Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In eubacteria, recycling is catalyzed by RRF (ribosome recycling factor) and EF-G (elongation factor G). By using cryo-electron microscopy, we have obtained two density maps, one of the RRF bound posttermination complex and one of the 50S subunit bound with both EF-G and RRF. Comparing the two maps, we found domain I of RRF to be in the same orientation, while domain II in the EF-G-containing 50S subunit is extensively rotated (approximately 60 degrees) compared to its orientation in the 70S complex. Mapping the 50S conformation of RRF onto the 70S posttermination complex suggests that it can disrupt the intersubunit bridges B2a and B3, and thus effect a separation of the two subunits. These observations provide the structural basis for the mechanism by which the posttermination complex is split into subunits by the joint action of RRF and EF-G.
History
DepositionMay 11, 2005-
Header (metadata) releaseMay 11, 2005-
Map releaseMay 11, 2006-
UpdateOct 31, 2012-
Current statusOct 31, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 60
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 60
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1zn0, PDB-1zn1
  • Surface level: 60
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1zn0
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1zn1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1127.gif

Downloads & links

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Map

FileDownload / File: emd_1127.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 50S.EF-G.GDPNP.RRF complex from E.coli
Voxel sizeX=Y=Z: 2.82 Å
Density
Contour Level1: 55.299999999999997 / Movie #1: 60
Minimum - Maximum-123.870000000000005 - 336.36099999999999
Average (Standard dev.)3.60572 (±29.409500000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-65
Dimensions130130130
Spacing130130130
CellA=B=C: 366.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.822.822.82
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z366.600366.600366.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-123.870336.3613.606

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Supplemental data

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Sample components

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Entire : 50S.EF-G.GDPNP.RRF complex from E.coli

EntireName: 50S.EF-G.GDPNP.RRF complex from E.coli
Components
  • Sample: 50S.EF-G.GDPNP.RRF complex from E.coli
  • Complex: 50S subunitProkaryotic large ribosomal subunit
  • Protein or peptide: RRF
  • Protein or peptide: EF-G

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Supramolecule #1000: 50S.EF-G.GDPNP.RRF complex from E.coli

SupramoleculeName: 50S.EF-G.GDPNP.RRF complex from E.coli / type: sample / ID: 1000 / Number unique components: 3

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Supramolecule #1: 50S subunit

SupramoleculeName: 50S subunit / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: RRF

MacromoleculeName: RRF / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #2: EF-G

MacromoleculeName: EF-G / type: protein_or_peptide / ID: 2 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: polymix buffer
StainingType: NEGATIVE / Details: Cryo-EM
GridDetails: Quantifoil holley carbon film grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: two-sided blotting plunger
Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.8 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 93 K
DateFeb 1, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Average electron dose: 15 e/Å2 / Od range: 1.2 / Bits/pixel: 12
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: defocus groups
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: Amplitude correction was applied using low-angle x-ray scattering data.
Number images used: 32171

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