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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: 1127
TitleMechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Sample50S.EF-G.GDPNP.RRF complex from E.coli
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataThis is a 50S.EF-G.GDPNP.RRF complex from E.coli
Methodsingle particle reconstruction, at 15.5 A resolution
AuthorsGao N / Zavialov AV / Li W / Sengupta J / Valle M / Gursky RP / Ehrenberg M / Frank J
CitationMol. Cell, 2005, 18, 663-674

Mol. Cell, 2005, 18, 663-674 StrPapers
Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Ning Gao / Andrey V Zavialov / Wen Li / Jayati Sengupta / Mikel Valle / Richard P Gursky / Måns Ehrenberg / Joachim Frank

DateDeposition: May 11, 2005 / Header (metadata) release: May 11, 2005 / Map release: May 11, 2006 / Last update: May 11, 2005

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 60
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 60
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1127.map.gz (map file in CCP4 format, 8584 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
2.82 A/pix
= 366.6 A
130 pix
2.82 A/pix
= 366.6 A
130 pix
2.82 A/pix
= 366.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.82 A
Density
Contour Level:55.3, 60 (movie #1):
Minimum - Maximum-123.87 - 336.361
Average (Standard dev.)3.60572 (29.4095)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions130130130
Origin-65-65-65
Limit646464
Spacing130130130
CellA=B=C: 366.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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 / Number of components: 3

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Component #1: ribosome-prokaryote, 50S subunit

Ribosome-prokaryoteName: 50S subunit / Prokaryote: LSU 50S / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, RRF

ProteinName: RRF / Recombinant expression: No / Number of Copies: 1
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: protein, EF-G

ProteinName: EF-G / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: polymix buffer / pH: 7.5
Support filmQuantifoil holley carbon film grids
StainingCryo-EM
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 90 % / Method: Blot for 2 seconds before plunging
Details: Vitrification instrument: two-sided blotting plunger

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Feb 1, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 49700 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4800 nm
Specimen HolderHolder: Cryo transfer / Model: GATAN LIQUID NITROGEN / Temperature: 93 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisition
14
Image acquisition
12
Image acquisition
12
Image acquisition
ZEISSSCAI

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 32171 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: reference projection / Software: SPIDER / CTF correction: defocus groups / Resolution: 15.5 A / Resolution method: FSC 0.5
Details: Amplitude correction was applied using low-angle x-ray scattering data.

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Atomic model buiding

Output model

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