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Yorodumi- EMDB-1901: Insights into the structure of the CCR4-NOT Complex by electron m... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1901 | |||||||||
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Title | Insights into the structure of the CCR4-NOT Complex by electron microscopy | |||||||||
Map data | Map of the stained Ccr4Not core-complex. | |||||||||
Sample |
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Keywords | Ccr4Not core-complex / regulation of gene-expression / deadenylation | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 33.0 Å | |||||||||
Authors | Nasertorabi F / Batisse C / Diepholz M / Suck D / Bottcher B | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1901.map.gz | 980.9 KB | EMDB map data format | |
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Header (meta data) | emd-1901-v30.xml emd-1901.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_1901.png | 135 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1901 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1901 | HTTPS FTP |
-Validation report
Summary document | emd_1901_validation.pdf.gz | 205.8 KB | Display | EMDB validaton report |
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Full document | emd_1901_full_validation.pdf.gz | 204.9 KB | Display | |
Data in XML | emd_1901_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1901 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1901 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1901.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of the stained Ccr4Not core-complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Ccr4Not core-complex
Entire | Name: Ccr4Not core-complex |
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Components |
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-Supramolecule #1000: Ccr4Not core-complex
Supramolecule | Name: Ccr4Not core-complex / type: sample / ID: 1000 / Details: Sample was fixed (Grafix) / Oligomeric state: Heterononamer / Number unique components: 1 |
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Molecular weight | Theoretical: 800 KDa |
-Macromolecule #1: Ccr4Not complex
Macromolecule | Name: Ccr4Not complex / type: protein_or_peptide / ID: 1 / Name.synonym: Ccr4Not complex / Details: The sample was fixed (Grafix) / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Staining | Type: NEGATIVE / Details: Sandwich negative staining with 2% uranyl acetate |
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Grid | Details: 400 mesh copper grid |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Temperature | Average: 295 K |
Alignment procedure | Legacy - Astigmatism: Corrected at 200,000 times magnification |
Image recording | Category: 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 max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 27500 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -55 |
-Image processing
Details | Initial reconstruction from random conical tilt data |
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Final reconstruction | Applied 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 |