+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32994 | |||||||||
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Title | Cryo-EM structure of IOC3-N2 nucleosome | |||||||||
Map data | IOC3-N2 nucleosome | |||||||||
Sample |
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Keywords | PROTEIN BINDING-DNA COMPLEX | |||||||||
Function / homology | Function and homology information Isw1 complex / Isw1a complex / sister chromatid cohesion / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae S288C (yeast) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||
Authors | Lifei L / Kangjing C / Chen Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structure of the ISW1a complex bound to the dinucleosome. Authors: Lifei Li / Kangjing Chen / Youyang Sia / Pengjing Hu / Youpi Ye / Zhucheng Chen / Abstract: Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin ...Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin organization and gene expression. Here we report the cryo-EM structure of chromatin remodeler ISW1a complex from Saccharomyces cerevisiae bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, while the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a and add a new mode of nucleosome remodeling in the context of a chromatin environment. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32994.map.gz | 7.1 MB | EMDB map data format | |
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Header (meta data) | emd-32994-v30.xml emd-32994.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
Images | emd_32994.png | 60.5 KB | ||
Filedesc metadata | emd-32994.cif.gz | 6.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32994 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32994 | HTTPS FTP |
-Validation report
Summary document | emd_32994_validation.pdf.gz | 353.8 KB | Display | EMDB validaton report |
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Full document | emd_32994_full_validation.pdf.gz | 353.3 KB | Display | |
Data in XML | emd_32994_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_32994_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32994 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32994 | HTTPS FTP |
-Related structure data
Related structure data | 7x3vMC 7x3tC 7x3wC 7x3xC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32994.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | IOC3-N2 nucleosome | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : IOC3-N2 nucleosome
+Supramolecule #1: IOC3-N2 nucleosome
+Supramolecule #2: N2 nucleosome
+Supramolecule #3: DNA
+Supramolecule #4: IOC3
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: ISWI one complex protein 3
+Macromolecule #5: DNA (146-MER)
+Macromolecule #6: DNA (146-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Relion3.0 |
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Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212026 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |