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- EMDB-25479: 2.3 A structure of the ATP-dependent chromatin remodeler Chd1 bou... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-25479 | |||||||||
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Title | 2.3 A structure of the ATP-dependent chromatin remodeler Chd1 bound to the nucleosome in a nucleotide-free state | |||||||||
![]() | Sharpened 2.3A map with a negative bfactor (-30) in an orientation aligned to a common reference. | |||||||||
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![]() | CHD1 / chromatin remodeling / ATPase / DBD / nucleosome / remodeling / transcription / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / sister chromatid cohesion / ATP-dependent chromatin remodeler activity ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / SAGA complex / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / methylated histone binding / helicase activity / transcription elongation by RNA polymerase II / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via homologous recombination / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / site of double-strand break / histone binding / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
![]() | Nodelman IM / Das S / Faustino AM / Fried SD / Bowman GD / Armache J-P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state. Authors: Ilana M Nodelman / Sayan Das / Anneliese M Faustino / Stephen D Fried / Gregory D Bowman / Jean-Paul Armache / ![]() Abstract: Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. Here we report a complex of the Chd1 remodeler bound to a nucleosome in a nucleotide-free ...Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. Here we report a complex of the Chd1 remodeler bound to a nucleosome in a nucleotide-free state, determined by cryo-EM to 2.3 Å resolution. The remodeler stimulates the nucleosome to absorb an additional nucleotide on each strand at two different locations: on the tracking strand within the ATPase binding site and on the guide strand one helical turn from the ATPase motor. Remarkably, the additional nucleotide on the tracking strand is associated with a local transformation toward an A-form geometry, explaining how sequential ratcheting of each DNA strand occurs. The structure also reveals a histone-binding motif, ChEx, which can block opposing remodelers on the nucleosome and may allow Chd1 to participate in histone reorganization during transcription. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 64.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.7 KB 24.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.1 KB | Display | ![]() |
Images | ![]() | 78.2 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 5.2 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 27.9 MB 672 KB 1.4 MB 116 MB 116 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 868.1 KB | Display | ![]() |
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Full document | ![]() | 867.6 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7swyMC ![]() 7tn2MC ![]() 25484 C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 4.7 TB Data #1: Unaligned frames of Chd1-bound nucleosomes collected on Gatan K3 in Super Resolution [micrographs - multiframe] Data #2: MotionCor2-aligned frames of Chd1-bound nucleosomes collected on Gatan K3 [micrographs - single frame] Data #3: Processed subsets [picked particles - single frame - processed]) |
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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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Annotation | Sharpened 2.3A map with a negative bfactor (-30) in an orientation aligned to a common reference. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.972 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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Density Histograms |
-Additional map: Unsharpened 2.3A map in an orientation aligned to a common reference.
File | emd_25479_additional_1.map | ||||||||||||
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Annotation | Unsharpened 2.3A map in an orientation aligned to a common reference. | ||||||||||||
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Density Histograms |
-Additional map: FSC Mask from cryoSPARC (before auto-tightening)
File | emd_25479_additional_2.map | ||||||||||||
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Annotation | FSC Mask from cryoSPARC (before auto-tightening) | ||||||||||||
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Density Histograms |
-Additional map: Refine Mask from cryoSPARC
File | emd_25479_additional_3.map | ||||||||||||
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Annotation | Refine Mask from cryoSPARC | ||||||||||||
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Density Histograms |
-Half map: half-map 1 (half A) from cryoSPARC
File | emd_25479_half_map_1.map | ||||||||||||
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Annotation | half-map 1 (half_A) from cryoSPARC | ||||||||||||
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Density Histograms |
-Half map: half-map 2 (half B) from cryoSPARC
File | emd_25479_half_map_2.map | ||||||||||||
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Annotation | half-map 2 (half_B) from cryoSPARC | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a...
Entire | Name: Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state |
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Components |
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-Supramolecule #1: Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a...
Supramolecule | Name: Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state type: complex / ID: 1 / Parent: 0 / Details: This entry has a weak DNA-binding domain |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 400 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.7 mg/mL |
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Buffer | pH: 7 Details: 20 mM HEPES, pH 7.0, 60 mM KCl, 1.5 mM DTT, 1 mM MgCl2 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | Nucleosome-bound CHD1, prepared in the presence of ATPgammaS, and then crosslinked using GraFix. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 6906 / Average exposure time: 3.3 sec. / Average electron dose: 49.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 28.0 µm / Calibrated defocus min: 4.0 µm / Calibrated magnification: 46296 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Details | phenix.real_space_refine | ||||||
Refinement | Space: REAL / Protocol: OTHER | ||||||
Output model | ![]() PDB-7swy: ![]() PDB-7tn2: |