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Yorodumi- EMDB-1878: CryoEM structure of the remodelling factor ISW1a bound to a monon... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1878 | |||||||||
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Title | CryoEM structure of the remodelling factor ISW1a bound to a mononucleosome (45N0) | |||||||||
Map data | Surface rendering of 2x45N0-ISW1a (delta ATPase) | |||||||||
Sample |
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Keywords | Chromatin remodelling factor / ISW1a / ISWI / nucleosome | |||||||||
Biological species | Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 24.0 Å | |||||||||
Authors | Frouws TD / Richmond TJ | |||||||||
Citation | Journal: Nature / Year: 2011 Title: Structure and mechanism of the chromatin remodelling factor ISW1a. Authors: Kazuhiro Yamada / Timothy D Frouws / Brigitte Angst / Daniel J Fitzgerald / Carl DeLuca / Kyoko Schimmele / David F Sargent / Timothy J Richmond / Abstract: Site-specific recognition of DNA in eukaryotic organisms depends on the arrangement of nucleosomes in chromatin. In the yeast Saccharomyces cerevisiae, ISW1a and related chromatin remodelling factors ...Site-specific recognition of DNA in eukaryotic organisms depends on the arrangement of nucleosomes in chromatin. In the yeast Saccharomyces cerevisiae, ISW1a and related chromatin remodelling factors are implicated in establishing the nucleosome repeat during replication and altering nucleosome position to affect gene activity. Here we have solved the crystal structures of S. cerevisiae ISW1a lacking its ATPase domain both alone and with DNA bound at resolutions of 3.25 Å and 3.60 Å, respectively, and we have visualized two different nucleosome-containing remodelling complexes using cryo-electron microscopy. The composite X-ray and electron microscopy structures combined with site-directed photocrosslinking analyses of these complexes suggest that ISW1a uses a dinucleosome substrate for chromatin remodelling. Results from a remodelling assay corroborate the dinucleosome model. We show how a chromatin remodelling factor could set the spacing between two adjacent nucleosomes acting as a 'protein ruler'. | |||||||||
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_1878.map.gz | 6.8 MB | EMDB map data format | |
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Header (meta data) | emd-1878-v30.xml emd-1878.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | EMD-1878image.png | 84.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1878 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1878 | HTTPS FTP |
-Validation report
Summary document | emd_1878_validation.pdf.gz | 228.1 KB | Display | EMDB validaton report |
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Full document | emd_1878_full_validation.pdf.gz | 227.3 KB | Display | |
Data in XML | emd_1878_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1878 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1878 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1878.map.gz / Format: CCP4 / Size: 17.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Surface rendering of 2x45N0-ISW1a (delta ATPase) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.78 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 : Chromatin remodelling factor ISW1a (delta ATPase) bound to a mono...
Entire | Name: Chromatin remodelling factor ISW1a (delta ATPase) bound to a mononucleosome (with a single 45 bp extension). This complex then forms a dimer. |
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Components |
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-Supramolecule #1000: Chromatin remodelling factor ISW1a (delta ATPase) bound to a mono...
Supramolecule | Name: Chromatin remodelling factor ISW1a (delta ATPase) bound to a mononucleosome (with a single 45 bp extension). This complex then forms a dimer. type: sample / ID: 1000 Details: 45 bp segments bridge 2 DNA binding sites across the 2-fold axis, resulting in the auto-dimerisation. Oligomeric state: Dimer / Number unique components: 2 |
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Molecular weight | Theoretical: 716 KDa |
-Macromolecule #1: Nucleosome
Macromolecule | Name: Nucleosome / type: protein_or_peptide / ID: 1 / Name.synonym: Nucleosome (45N0) Details: Recombinant Xenopus histones H2A,H2B,H3,H4 are reconstituted onto a nucleosome containing the '601' positioning sequence and a single 45 bp extension. Recombinant expression: Yes |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 250 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #2: ISW1a
Macromolecule | Name: ISW1a / type: protein_or_peptide / ID: 2 / Name.synonym: Remodelling factor Details: Recombinant Yeast ISW1a (delta ATPase) is expressed in the MultiBac system Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 120 MDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.5 mg/mL |
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Buffer | pH: 7.5 / Details: 10mM TrisCl, 10mM KCl, 0,1 mM EDTA |
Grid | Details: C-flat 224 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK II / Details: Vitrification instrument: Vitribot MKII / Method: Offset 0, Blot 4 sec, Drain 1 sec |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 100 K |
Details | low dose |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 107520 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | Manually fit using Chimera and "sym" command to impose 2-fold symmetry. Missing DNA segments were manually built in. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |