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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10059 | |||||||||||||||
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Title | Nucleosome-CHD4 complex structure (two CHD4 copies) | |||||||||||||||
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![]() | Complex / ATPase / chromatin / nucleosome / CHD family / TRANSCRIPTION | |||||||||||||||
Function / homology | ![]() cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / regulation of stem cell differentiation / NuRD complex / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / site of DNA damage / RNA Polymerase I Transcription Initiation ...cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / regulation of stem cell differentiation / NuRD complex / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / site of DNA damage / RNA Polymerase I Transcription Initiation / Regulation of TP53 Activity through Acetylation / helicase activity / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / transcription coregulator binding / HDACs deacetylate histones / double-strand break repair via homologous recombination / histone deacetylase binding / RNA polymerase II transcription regulator complex / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / histone binding / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||||||||
![]() | Farnung L / Ochmann M | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Nucleosome-CHD4 chromatin remodeler structure maps human disease mutations. Authors: Lucas Farnung / Moritz Ochmann / Patrick Cramer / ![]() Abstract: Chromatin remodeling plays important roles in gene regulation during development, differentiation and in disease. The chromatin remodeling enzyme CHD4 is a component of the NuRD and ChAHP complexes ...Chromatin remodeling plays important roles in gene regulation during development, differentiation and in disease. The chromatin remodeling enzyme CHD4 is a component of the NuRD and ChAHP complexes that are involved in gene repression. Here, we report the cryo-electron microscopy (cryo-EM) structure of CHD4 engaged with a nucleosome core particle in the presence of the non-hydrolysable ATP analogue AMP-PNP at an overall resolution of 3.1 Å. The ATPase motor of CHD4 binds and distorts nucleosomal DNA at superhelical location (SHL) +2, supporting the 'twist defect' model of chromatin remodeling. CHD4 does not induce unwrapping of terminal DNA, in contrast to its homologue Chd1, which functions in gene activation. Our structure also maps CHD4 mutations that are associated with human cancer or the intellectual disability disorder Sifrim-Hitz-Weiss syndrome. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 30.9 KB 30.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 67.5 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 7.9 KB | ||
Others | ![]() ![]() ![]() ![]() | 80.4 MB 95.9 MB 80.8 MB 80.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 877.7 KB | Display | ![]() |
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Full document | ![]() | 877.2 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ryuMC ![]() 6ryrC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 721.2 Data #1: Unaligned multi-frame micrographs of NCP-CHD4 Dataset 1 [micrographs - multiframe] Data #2: Averaged and aligned micrographs Dataset 1 [micrographs - single frame] Data #3: Unaligned multi-frame micrographs of NCP-CHD4 Dataset 2 [micrographs - multiframe] Data #4: Averaged and aligned micrographs NCP-CHD4 Dataset 2 [micrographs - single frame] Data #5: Unaligned multi-frame micrographs of NCP-CHD4 Dataset 3 [micrographs - multiframe] Data #6: Averaged and aligned micrographs Dataset 3 [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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-Additional map: #1
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-Additional map: #2
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-Half map: #2
File | emd_10059_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_10059_half_map_2.map | ||||||||||||
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Sample components
+Entire : Nucleosome-CHD4 complex
+Supramolecule #1: Nucleosome-CHD4 complex
+Supramolecule #2: Histone
+Supramolecule #3: DNA
+Supramolecule #4: Chromodomain-helicase-DNA-binding protein 4
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: Chromodomain-helicase-DNA-binding protein 4,CHD4,Chromodomain-hel...
+Macromolecule #5: DNA (149-MER)
+Macromolecule #6: DNA (149-MER)
+Macromolecule #8: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |