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- EMDB-1918: Binding conformations and positions of RRF and EF-G during interm... -

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Basic information

Entry
Database: EMDB / ID: EMD-1918
TitleBinding conformations and positions of RRF and EF-G during intermediate state of ribosome recycling
Map dataT. thermophilus Ribosome Recycling Factor and E. coli Elongation Factor G
Sample
  • Sample: T. thermophilus Ribosome Recycling Factor and E. coli Elongation Factor G
  • Protein or peptide: T. thermophilus Ribosome Recycling Factor
  • Protein or peptide: E. coli Elongation Factor G
KeywordsRibosome recycling factor / Elongation Factor G / T. thermophilus ribosome recycling factor / 70S / E. coli Post-Termination Complex / cryo-EM
Function / homology
Function and homology information


ribosome disassembly / guanosine tetraphosphate binding / ribosomal large subunit binding / translational elongation / misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / translational termination / positive regulation of RNA splicing ...ribosome disassembly / guanosine tetraphosphate binding / ribosomal large subunit binding / translational elongation / misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / translational termination / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / GTPase activity / GTP binding / cytoplasm / cytosol
Similarity search - Function
Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III ...Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S12, bacterial-type / Small GTP-binding protein domain / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Elongation factor G / Small ribosomal subunit protein uS12 / Ribosome-recycling factor
Similarity search - Component
Biological speciesThermus thermophilus (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.9 Å
AuthorsYokoyama T / Shaikh TR / Iwakura N / Kaji H / Kaji A / Agrawal RK
CitationJournal: EMBO J / Year: 2012
Title: Structural insights into initial and intermediate steps of the ribosome-recycling process.
Authors: Takeshi Yokoyama / Tanvir R Shaikh / Nobuhiro Iwakura / Hideko Kaji / Akira Kaji / Rajendra K Agrawal /
Abstract: The ribosome-recycling factor (RRF) and elongation factor-G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-electron ...The ribosome-recycling factor (RRF) and elongation factor-G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-electron microscopic structures of the PoTC·RRF complex, with and without EF-G. We find that domain II of RRF initially interacts with universally conserved residues of the 23S rRNA helices 43 and 95, and protein L11 within the 50S ribosomal subunit. Upon EF-G binding, both RRF and tRNA are driven towards the tRNA-exit (E) site, with a large rotational movement of domain II of RRF towards the 30S ribosomal subunit. During this intermediate step of the recycling process, domain II of RRF and domain IV of EF-G adopt hitherto unknown conformations. Furthermore, binding of EF-G to the PoTC·RRF complex reverts the ribosome from ratcheted to unratcheted state. These results suggest that (i) the ribosomal intersubunit reorganizations upon RRF binding and subsequent EF-G binding could be instrumental in destabilizing the PoTC and (ii) the modes of action of EF-G during tRNA translocation and ribosome-recycling steps are markedly different.
History
DepositionJun 29, 2011-
Header (metadata) releaseJul 22, 2011-
Map releaseApr 27, 2012-
UpdateSep 10, 2014-
Current statusSep 10, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j0e
  • Surface level: 13
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1918.tif

Downloads & links

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Map

FileDownload / File: emd_1918.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT. thermophilus Ribosome Recycling Factor and E. coli Elongation Factor G
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.78 Å/pix.
x 130 pix.
= 361.4 Å		2.78 Å/pix.
x 130 pix.
= 361.4 Å		2.78 Å/pix.
x 130 pix.
= 361.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 6.43 / Movie #1: 13
Minimum - Maximum-9.119332310000001 - 57.060966489999998
Average (Standard dev.)0.1077323 (±1.93141139)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions130130130
Spacing130130130
CellA=B=C: 361.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.782.782.78
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z361.400361.400361.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean-9.11957.0610.108

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Supplemental data

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Sample components

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Entire : T. thermophilus Ribosome Recycling Factor and E. coli Elongation ...

EntireName: T. thermophilus Ribosome Recycling Factor and E. coli Elongation Factor G
Components
  • Sample: T. thermophilus Ribosome Recycling Factor and E. coli Elongation Factor G
  • Protein or peptide: T. thermophilus Ribosome Recycling Factor
  • Protein or peptide: E. coli Elongation Factor G

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Supramolecule #1000: T. thermophilus Ribosome Recycling Factor and E. coli Elongation ...

SupramoleculeName: T. thermophilus Ribosome Recycling Factor and E. coli Elongation Factor G
type: sample / ID: 1000 / Oligomeric state: Monomer / Number unique components: 2
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: T. thermophilus Ribosome Recycling Factor

MacromoleculeName: T. thermophilus Ribosome Recycling Factor / type: protein_or_peptide / ID: 1 / Name.synonym: ttRRF
Details: This is the excised density corresponding to Thermus thermophilus RRF and E. coli EF-G from the parent map EMD-1917.
Recombinant expression: Yes
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 100 KDa
Recombinant expressionOrganism: Escherichia coli JM109 / Recombinant plasmid: pGEM-T

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Macromolecule #2: E. coli Elongation Factor G

MacromoleculeName: E. coli Elongation Factor G / type: protein_or_peptide / ID: 2 / Name.synonym: ecEFG
Details: This is the excised density corresponding to Thermus thermophilus RRF and E. coli EF-G from the parent map EMD-1917.
Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 100 KDa
Recombinant expressionOrganism: Escherichia coli JM83 / Recombinant plasmid: pUC3G

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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 / Details: 50mM Tris-HCl (pH 7.5), 10mM Mg(OAc)2, 25mM KCl
GridDetails: 300 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 80 K
Alignment procedureLegacy - Astigmatism: Objective correct at 200,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 383 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50310 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen cooled cryo holder
Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 338823

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Atomic model buiding 1

Initial modelPDB ID:

1eh1

SoftwareName: MDFF
DetailsProtocol: Flexible Fitting
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j0e:
Models for the T. thermophilus ribosome recycling factor and the E. coli elongation factor G bound to the E. coli post-termination complex

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