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- EMDB-1705: Mechanism of eIF6s anti-association activity -

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Basic information

Entry
Database: EMDB / ID: 1705
TitleMechanism of eIF6s anti-association activity
Keywords60S / ribosome / eIF6
Sample60S-eIF6 complex
SourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Map data60S-eIF6 complex from S. cerevisiae
Methodsingle particle reconstruction, at 11.8 Å resolution
AuthorsGartmann M / Blau M / Armache J-P / Mielke T / Topf M / Beckmann R
CitationJ. Biol. Chem., 2010, 285, 14848-14851

J. Biol. Chem., 2010, 285, 14848-14851 StrPapers
Mechanism of eIF6-mediated inhibition of ribosomal subunit joining.
Marco Gartmann / Michael Blau / Jean-Paul Armache / Thorsten Mielke / Maya Topf / Roland Beckmann

Validation ReportPDB-ID: 2x7n

SummaryFull reportAbout validation report
DateDeposition: Mar 1, 2010 / Header (metadata) release: Apr 26, 2011 / Map release: Apr 26, 2011 / Last update: Apr 16, 2014

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.024
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-2x7n
  • Surface level: 0.024
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-2x7n
  • Imaged by Jmol
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Supplemental images

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Map

Fileemd_1705.map.gz (map file in CCP4 format, 7095 KB)
Projections & slices

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AxesZ (Sec.)X (Row.)Y (Col.)
122 pix
3.71 Å/pix.
= 452.62 Å
122 pix
3.71 Å/pix.
= 452.62 Å
122 pix
3.71 Å/pix.
= 452.62 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.71 Å
Density
Contour Level:0.024 (by author), 0.024 (movie #1):
Minimum - Maximum-0.0433532 - 0.129382
Average (Standard dev.)0.00042245 (0.00940148)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions122122122
Origin-61-61-60
Limit606061
Spacing122122122
CellA=B=C: 452.62 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.713.713.71
M x/y/z122122122
origin x/y/z0.0000.0000.000
length x/y/z452.620452.620452.620
α/β/γ90.00090.00090.000
start NX/NY/NZ-61-61-60
NX/NY/NZ122122122
MAP C/R/S213
start NC/NR/NS-61-61-60
NC/NR/NS122122122
D min/max/mean-0.0430.1290.000

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Supplemental data

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Sample components

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Entire 60S-eIF6 complex

EntireName: 60S-eIF6 complex
Details: Reconstituted complex of 60S subunits with eIF6 in vitreous ice
Number of components: 2 / Oligomeric State: Heterodimer

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Component #1: ribosome-eukaryote, 60S

Ribosome-eukaryoteName: 60S / a.k.a: 60S ribosomal subunit / Details: 60S subunit, contains rpL23, rpL24 and SRL. / Eukaryote: LSU 60S

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Component #2: protein, EUKARYOTIC TRANSLATION INITIATION FACTOR 6

ProteinName: EUKARYOTIC TRANSLATION INITIATION FACTOR 6 / a.k.a: EIF-6 / Oligomeric Details: Monomer / Details: Residues 1-224 / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 25 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: NONE / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 39000 X (nominal), 38900 X (calibrated) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: FEI Polara cartridge system / Model: GATAN LIQUID NITROGEN / Temperature: K ( 95 - K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: PRIMESCAN

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: Spider / CTF correction: Defocus group volumes / Resolution: 11.8 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Flex-EM / Refinement space: REAL
Input PDB model: 1G62
Chain ID: 1G62_A
Output model

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