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- EMDB-1901: Insights into the structure of the CCR4-NOT Complex by electron m... -

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Basic information

Entry
Database: EMDB / ID: EMD-1901
TitleInsights into the structure of the CCR4-NOT Complex by electron microscopy
Map dataMap of the stained Ccr4Not core-complex.
Sample
  • Sample: Ccr4Not core-complex
  • Protein or peptide: Ccr4Not complex
KeywordsCcr4Not core-complex / regulation of gene-expression / deadenylation
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 33.0 Å
AuthorsNasertorabi F / Batisse C / Diepholz M / Suck D / Bottcher B
CitationJournal: FEBS Lett / Year: 2011
Title: Insights into the structure of the CCR4-NOT complex by electron microscopy.
Authors: Fariborz Nasertorabi / Claire Batisse / Meikel Diepholz / Dietrich Suck / Bettina Böttcher /
Abstract: The CCR4-NOT complex is a deadenylation complex, which plays a major role for mRNA stability. The complex is conserved from yeast to human and consists of nine proteins NOT1-NOT5, CCR4, CAF1, CAF40 ...The CCR4-NOT complex is a deadenylation complex, which plays a major role for mRNA stability. The complex is conserved from yeast to human and consists of nine proteins NOT1-NOT5, CCR4, CAF1, CAF40 and CAF130. We have successfully isolated the complex using a Protein A tag on NOT1, followed by cross-linking on a glycerol gradient. All components of the complex were identified by mass spectrometry. Electron microscopy of negatively stained particles followed by image reconstruction revealed an L-shaped complex with two arms of similar length. The arms form an accessible cavity, which we think could provide an extensive interface for RNA-deadenylation.
History
DepositionMay 25, 2011-
Header (metadata) releaseJun 10, 2011-
Map releaseJun 10, 2011-
UpdateSep 9, 2011-
Current statusSep 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.46
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.46
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1901.png

Downloads & links

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Map

FileDownload / File: emd_1901.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the stained Ccr4Not core-complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.2 Å/pix.
x 80 pix.
= 416. Å		5.2 Å/pix.
x 80 pix.
= 416. Å		5.2 Å/pix.
x 80 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46 / Movie #1: 0.46
Minimum - Maximum-0.326318 - 2.22817
Average (Standard dev.)0.00062974 (±0.11313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 416 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z808080
origin x/y/z-0.000-0.000-0.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.3262.2280.001

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Supplemental data

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Sample components

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Entire : Ccr4Not core-complex

EntireName: Ccr4Not core-complex
Components
  • Sample: Ccr4Not core-complex
  • Protein or peptide: Ccr4Not complex

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Supramolecule #1000: Ccr4Not core-complex

SupramoleculeName: Ccr4Not core-complex / type: sample / ID: 1000 / Details: Sample was fixed (Grafix) / Oligomeric state: Heterononamer / Number unique components: 1
Molecular weightTheoretical: 800 KDa

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Macromolecule #1: Ccr4Not complex

MacromoleculeName: Ccr4Not complex / type: protein_or_peptide / ID: 1 / Name.synonym: Ccr4Not complex / Details: The sample was fixed (Grafix) / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE / Details: Sandwich negative staining with 2% uranyl acetate
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 295 K
Alignment procedureLegacy - Astigmatism: Corrected at 200,000 times magnification
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 14.5 µm / Number real images: 312
Details: Micrographs were taken in pairs for random-conical tilt reconstruction
Bits/pixel: 12
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 27500
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -55

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Image processing

DetailsInitial reconstruction from random conical tilt data
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider, imagic, xmipp / Number images used: 7000

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