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- EMDB-1366: Locking and unlocking of ribosomal motions. -

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Basic information

Entry
Database: EMDB / ID: 1366
TitleLocking and unlocking of ribosomal motions.
SampleEF-G bound Release Complex in the presence of Puromycin and GTP
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Synthetic construct
Map dataCryo-EM map of E.coli 70S ribosome
Methodsingle particle reconstruction, at 12.8 A resolution
AuthorsMikel V / Andrey Z / Sengupta J / Rawat U / Ehrenberg M / Frank J
CitationCell, 2003, 114, 123-134

Cell, 2003, 114, 123-134 StrPapers
Locking and unlocking of ribosomal motions.
Mikel Valle / Andrey Zavialov / Jayati Sengupta / Urmila Rawat / Måns Ehrenberg / Joachim Frank

DateDeposition: May 22, 2007 / Header (metadata) release: May 24, 2007 / Map release: May 24, 2007 / Last update: May 22, 2007

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 30
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-1pn6
  • Surface level: 30
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1366.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:57.3, 30 (movie #1):
Minimum - Maximum-118.471 - 239.101
Average (Standard dev.)2.85556 (25.5653)
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-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-118.471239.1012.856

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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 and GTP

EntireName: EF-G bound Release Complex in the presence of Puromycin and GTP
Number of components: 4

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Component #1: ribosome-prokaryote, Release Complex

Ribosome-prokaryoteName: Release Complex / Details: mRNA, tRNA / Prokaryote: ALL / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: MRE600

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Component #2: ligand, Puromycin

LigandName: Puromycin / Details: Antibiotic / Recombinant expression: No
SourceSpecies: Synthetic construct

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Component #3: ligand, EF-G

LigandName: EF-G / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: MRE600

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Component #4: ligand, GTP

LigandName: GTP / Recombinant expression: No
SourceSpecies: Synthetic construct

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: NONE / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Jul 11, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: cryo transfer / Model: GATAN LIQUID NITROGEN / Temperature: 93 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: ZEISS SCAI / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Back projection / Software: SPIDER, package / CTF correction: CTF correctionn of 3D map / Resolution: 12.8 A / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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