+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30298 | |||||||||
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Title | CryoEM structure of CHD7(N-CRD) bound to the nucleosome | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.25 Å | |||||||||
Authors | Lee E / Song JJ | |||||||||
Funding support | Korea, Republic Of, 2 items
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Citation | Journal: J Mol Biol / Year: 2021 Title: A Novel N-terminal Region to Chromodomain in CHD7 is Required for the Efficient Remodeling Activity. Authors: Eunhye Lee / Chanshin Kang / Pasi Purhonen / Hans Hebert / Karim Bouazoune / Sungchul Hohng / Ji-Joon Song / Abstract: Chromodomain-Helicase DNA binding protein 7 (CHD7) is an ATP dependent chromatin remodeler involved in maintaining open chromatin structure. Mutations of CHD7 gene causes multiple developmental ...Chromodomain-Helicase DNA binding protein 7 (CHD7) is an ATP dependent chromatin remodeler involved in maintaining open chromatin structure. Mutations of CHD7 gene causes multiple developmental disorders, notably CHARGE syndrome. However, there is not much known about the molecular mechanism by which CHD7 remodels nucleosomes. Here, we performed biochemical and biophysical analysis on CHD7 chromatin remodeler and uncover that N-terminal to the Chromodomain (N-CRD) interacts with nucleosome and contains a high conserved arginine stretch, which is reminiscent of arginine anchor. Importantly, this region is required for efficient ATPase stimulation and nucleosome remodeling activity of CHD7. Furthermore, smFRET analysis shows the mutations in the N-CRD causes the defects in remodeling activity. Collectively, our results uncover the functional importance of a previously unidentified N-terminal region in CHD7 and implicate that the multiple domains in chromatin remodelers are involved in regulating their activities. | |||||||||
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_30298.map.gz | 5.5 MB | EMDB map data format | |
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Header (meta data) | emd-30298-v30.xml emd-30298.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30298_fsc.xml | 8.3 KB | Display | FSC data file |
Images | emd_30298.png | 33.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30298 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30298 | HTTPS FTP |
-Validation report
Summary document | emd_30298_validation.pdf.gz | 350.4 KB | Display | EMDB validaton report |
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Full document | emd_30298_full_validation.pdf.gz | 350 KB | Display | |
Data in XML | emd_30298_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | emd_30298_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30298 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30298 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30298.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 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 : CryoEM structure of CHD7 bound to the nucleosome
+Supramolecule #1: CryoEM structure of CHD7 bound to the nucleosome
+Supramolecule #2: CHD7
+Supramolecule #3: Histone H3, H4, H2A, H2B
+Supramolecule #4: DNA
+Macromolecule #1: Chromodomain Helicase DNA binding Protein 7( CHD7 )
+Macromolecule #2: Histone H3
+Macromolecule #3: Histone H4
+Macromolecule #4: Histone H2A
+Macromolecule #5: Histone H2B
+Macromolecule #6: widom 601 DNA sequence
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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 K2 SUMMIT (4k x 4k) / Average electron dose: 47.94 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |