+Open data
-Basic information
Entry | Database: PDB / ID: 6ryr | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Nucleosome-CHD4 complex structure (single CHD4 copy) | |||||||||||||||
Components |
| |||||||||||||||
Keywords | TRANSCRIPTION / Complex / ATPase / chromatin / nucleosome / CHD family | |||||||||||||||
Function / homology | Function and homology information cerebellar granule cell to Purkinje cell synapse / terminal button organization / NuRD complex / regulation of cell fate specification / regulation of stem cell differentiation / 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 / NuRD complex / regulation of cell fate specification / regulation of stem cell differentiation / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / site of DNA damage / RNA Polymerase I Transcription Initiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Regulation of TP53 Activity through Acetylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Regulation of PTEN gene transcription / helicase activity / 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 | Xenopus laevis (African clawed frog) synthetic construct (others) Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Farnung, L. / Ochmann, M. / Cramer, P. | |||||||||||||||
Funding support | Germany, 4items
| |||||||||||||||
Citation | Journal: Elife / Year: 2020 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ryr.cif.gz | 443.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ryr.ent.gz | 324.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ryr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ryr_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ryr_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6ryr_validation.xml.gz | 57.9 KB | Display | |
Data in CIF | 6ryr_validation.cif.gz | 89.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/6ryr ftp://data.pdbj.org/pub/pdb/validation_reports/ry/6ryr | HTTPS FTP |
-Related structure data
Related structure data | 10058MC 6ryuC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10411 (Title: Single Particle Cryo-EM Reconstructions of NCP-CHD4 complexes 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]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 5 types, 9 molecules AEBFCGDHW
#1: Protein | Mass: 15435.126 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 14109.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897 #4: Protein | Mass: 13655.948 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 #7: Protein | | Mass: 219628.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHD4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14839, DNA helicase |
---|
-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 45781.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
---|---|
#6: DNA chain | Mass: 46203.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 3 types, 4 molecules
#8: Chemical | ChemComp-ANP / |
---|---|
#9: Chemical | ChemComp-MG / |
#10: Chemical |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 43 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18_3855: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89623 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|