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- EMDB-1365: Locking and unlocking of ribosomal motions. -

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Basic information

Entry
Database: EMDB / ID: EMD-1365
TitleLocking and unlocking of ribosomal motions.
Map dataCryo-EM map of E.coli 70S ribosome
Sample
  • Sample: EF-G bound Release Complex in the presence of Puromycin, GDP and fus
  • Complex: Release Complex
  • Ligand: Puromycin
  • Ligand: EF-G
  • Ligand: GDP
  • Ligand: Fusidic acid
Function / homology
Function and homology information


ribosome disassembly / translational elongation / translation elongation factor activity / GDP binding / ribosome binding / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding ...ribosome disassembly / translational elongation / translation elongation factor activity / GDP binding / ribosome binding / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / GTPase activity / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
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 ...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 / Ribosomal protein L11, bacterial-type / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / 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/L12 / Ribosomal protein L11, RNA binding domain / 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 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.75 Å
AuthorsMikel V / Andrey Z / Sengupta J / Rawat U / Ehrenberg M / Frank J
CitationJournal: Cell / Year: 2003
Title: Locking and unlocking of ribosomal motions.
Authors: Mikel Valle / Andrey Zavialov / Jayati Sengupta / Urmila Rawat / Måns Ehrenberg / Joachim Frank /
Abstract: During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the ...During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the direction of the mRNA movement. By means of cryo-electron microscopy we observe that this rotation is accompanied by a 20 A movement of the L1 stalk of the 50S subunit, implying that this region is involved in the translocation of deacylated tRNAs from the P to the E site. These ribosomal motions can occur only when the P-site tRNA is deacylated. Prior to peptidyl-transfer to the A-site tRNA or peptide removal, the presence of the charged P-site tRNA locks the ribosome and prohibits both of these motions.
History
DepositionMay 21, 2007-
Header (metadata) releaseMay 24, 2007-
Map releaseMay 24, 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: 35
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1pn6, PDB-1pn7, PDB-1pn8
  • Surface level: 35
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pn6
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pn7
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pn8
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1365.gif

Downloads & links

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Map

FileDownload / File: emd_1365.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of E.coli 70S ribosome
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

Histogram

Histogram (log scale)
Contour Level1: 55.700000000000003 / Movie #1: 35
Minimum - Maximum-134.064999999999998 - 279.725999999999999
Average (Standard dev.)2.55802 (±25.511500000000002)
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-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-134.065279.7262.558

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Supplemental data

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Sample components

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Entire : EF-G bound Release Complex in the presence of Puromycin, GDP and fus

EntireName: EF-G bound Release Complex in the presence of Puromycin, GDP and fus
Components
  • Sample: EF-G bound Release Complex in the presence of Puromycin, GDP and fus
  • Complex: Release Complex
  • Ligand: Puromycin
  • Ligand: EF-G
  • Ligand: GDP
  • Ligand: Fusidic acid

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Supramolecule #1000: EF-G bound Release Complex in the presence of Puromycin, GDP and fus

SupramoleculeName: EF-G bound Release Complex in the presence of Puromycin, GDP and fus
type: sample / ID: 1000 / Number unique components: 5

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Supramolecule #1: Release Complex

SupramoleculeName: Release Complex / type: complex / ID: 1 / Details: mRNA, tRNA / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600

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Macromolecule #1: Puromycin

MacromoleculeName: Puromycin / type: ligand / ID: 1 / Details: Antibiotic / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)
Chemical component information

ChemComp-PUY:
PUROMYCIN

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Macromolecule #2: EF-G

MacromoleculeName: EF-G / type: ligand / ID: 2 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600

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Macromolecule #3: GDP

MacromoleculeName: GDP / type: ligand / ID: 3 / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)

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Macromolecule #4: Fusidic acid

MacromoleculeName: Fusidic acid / type: ligand / ID: 4 / Details: Antibiotic / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)
Chemical component information

ChemComp-FUA:
FUSIDIC ACID / antibiotic*YM

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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 / Instrument: OTHER / Details: Rapid-freezing in liquid ethane

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Electron microscopy

MicroscopeFEI TECNAI 20
TemperatureAverage: 93 K
Alignment procedureLegacy - Electron beam tilt params: 0
DateJul 11, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN

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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: 11.75 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, package / Number images used: 1

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