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- EMDB-1430: Specific interaction between EF-G and RRF and its implication for... -

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Basic information

Entry
Database: EMDB / ID: EMD-1430
TitleSpecific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
Map dataCryo-EM map of E.coli 50S complex
Sample
  • Sample: 50S subunit with EF-G and RRF bound
  • Complex: 50S subunitProkaryotic large ribosomal subunit
  • Protein or peptide: EF-G
  • Protein or peptide: RRF
Function / homology
Function and homology information


cytoplasmic translational termination / ribosome disassembly / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / translational elongation / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...cytoplasmic translational termination / ribosome disassembly / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / translational elongation / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / negative regulation of translational initiation / translation repressor activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / translation elongation factor activity / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / : / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / negative regulation of DNA-templated transcription / GTP binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
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 / Ribosomal protein L1, bacterial-type / 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. / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L25, short-form / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L31 type A / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33
Similarity search - Domain/homology
Large ribosomal subunit protein uL15 / Elongation factor G / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 ...Large ribosomal subunit protein uL15 / Elongation factor G / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Ribosome-recycling factor / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsGao N / Zavialov A / Ehrenberg M / Frank J
CitationJournal: J Mol Biol / Year: 2007
Title: Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
Authors: Ning Gao / Andrey V Zavialov / Måns Ehrenberg / Joachim Frank /
Abstract: After termination of protein synthesis, the bacterial ribosome is split into its 30S and 50S subunits by the action of ribosome recycling factor (RRF) and elongation factor G (EF-G) in a guanosine 5'- ...After termination of protein synthesis, the bacterial ribosome is split into its 30S and 50S subunits by the action of ribosome recycling factor (RRF) and elongation factor G (EF-G) in a guanosine 5'-triphosphate (GTP)-hydrolysis-dependent manner. Based on a previous cryo-electron microscopy study of ribosomal complexes, we have proposed that the binding of EF-G to an RRF-containing posttermination ribosome triggers an interdomain rotation of RRF, which destabilizes two strong intersubunit bridges (B2a and B3) and, ultimately, separates the two subunits. Here, we present a 9-A (Fourier shell correlation cutoff of 0.5) cryo-electron microscopy map of a 50S x EF-G x guanosine 5'-[(betagamma)-imido]triphosphate x RRF complex and a quasi-atomic model derived from it, showing the interaction between EF-G and RRF on the 50S subunit in the presence of the noncleavable GTP analogue guanosine 5'-[(betagamma)-imido]triphosphate. The detailed information in this model and a comparative analysis of EF-G structures in various nucleotide- and ribosome-bound states show how rotation of the RRF head domain may be triggered by various domains of EF-G. For validation of our structural model, all known mutations in EF-G and RRF that relate to ribosome recycling have been taken into account. More importantly, our results indicate a substantial conformational change in the Switch I region of EF-G, suggesting that a conformational signal transduction mechanism, similar to that employed in transfer RNA translocation on the ribosome by EF-G, translates a large-scale movement of EF-G's domain IV, induced by GTP hydrolysis, into the domain rotation of RRF that eventually splits the ribosome into subunits.
History
DepositionSep 24, 2007-
Header (metadata) releaseSep 24, 2007-
Map releaseDec 12, 2007-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 56.11285599
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 56.11285599
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2rdo
  • Surface level: 56.11285599
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1430.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of E.coli 50S complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.82 Å/pix.
x 130 pix.
= 366.6 Å
2.82 Å/pix.
x 130 pix.
= 366.6 Å
2.82 Å/pix.
x 130 pix.
= 366.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.82 Å
Density
Contour Level1: 48.899999999999999 / Movie #1: 56.112856
Minimum - Maximum-81.8292 - 310.661999999999978
Average (Standard dev.)5.65535 (±24.203700000000001)
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/NZ000
NX/NY/NZ10110173
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-81.829310.6625.655

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Supplemental data

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Sample components

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Entire : 50S subunit with EF-G and RRF bound

EntireName: 50S subunit with EF-G and RRF bound
Components
  • Sample: 50S subunit with EF-G and RRF bound
  • Complex: 50S subunitProkaryotic large ribosomal subunit
  • Protein or peptide: EF-G
  • Protein or peptide: RRF

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Supramolecule #1000: 50S subunit with EF-G and RRF bound

SupramoleculeName: 50S subunit with EF-G and RRF bound / 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) / Strain: MRE600

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Macromolecule #1: EF-G

MacromoleculeName: EF-G / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600

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Macromolecule #2: RRF

MacromoleculeName: RRF / type: protein_or_peptide / ID: 2 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600

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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

BufferDetails: Polymix buffer
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Rapid-freezing in liquid ethane / Method: Vitrobot

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.9 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 50000
Sample stageSpecimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 93 K
Alignment procedureLegacy - Electron beam tilt params: 0
DateDec 14, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 259 / Average electron dose: 15 e/Å2
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTF correctionn of 3D map
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, package / Number images used: 113355

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