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TitleNucleosome-CHD4 complex structure (two CHD4 copies)
AuthorsFarnung L, Ochmann M
MethodSingle Particle(Reported Resolution 4 Å)PDB:6ryuNAKB:6ryuEMPIAR-10411
EMDB image
Primary CitationNucleosome-CHD4 chromatin remodeller structure maps human disease mutations. Farnung L, Ochmann M, Cramer P Elife (2020) PubMed DOI show all entries for this citation
Funding SourceGerman Research Foundation (DFG), European Research Council (ERC), Volkswagen Foundation
StatusDepositedReleasedLast Update
REL2019-06-122020-07-152024-05-22

Name: Nucleosome-CHD4 complexSpecimenType: particle MW: 0.642 MDa pH: 7.4

Component Typescomplex
Component Names

Chromodomain-helicase-DNA-binding protein 4

DNA

Histone

Molecular TypesDNA, ligand, protein
Molecule Names
  • Chromodomain-helicase-DNA-binding protein 4,CHD4,Chromodomain-helicase-DNA-binding protein 4
  • DNA (149-MER)
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • MAGNESIUM ION
  • PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • ZINC ION
Sources

synthetic construct ncbi:32630

Xenopus laevis ncbi:8355

Homo sapiens ncbi:9606

Ligand IDs: ANP MG ZN

Specimen Preparationvitrification
VitrificationFEI VITROBOT MARK IV
MicroscopeFEI TITAN KRIOS (300 kV)
Specimen HolderFEI TITAN KRIOS AUTOGRID HOLDER
DetectorGATAN K2 SUMMIT (4k x 4k)
Electron Dose43 (e/sq. Å)
Number of Particles40233
Imposed SymmetryC1
Reconstruction SoftwareRELION
Map File Size108 Mbytes
Voxel Dimensions (Å)1.05 x 1.05 x 1.05
Map Dimensions (voxels) 300 x 300 x 300
Map Data Type IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Density StatisticsMin -0.016Max 0.029Avg 0Std 0.001
Recommended Contour Level0.00472 (4.8 σ)
Mol*3DViewer Map Visual Analysis @ EMDB
wwPDB Map Validation Reportemd_10059_full_validation.pdf.gz
wwPDB Model Validation Report6ryu_full_validation.pdf.gz
View EMDB map entry EMD-10059: EMDB PDBj 3Dbionotes
View associated model PDB 6ryu: RCSB-PDB PDBe PDBj