- EMDB-25480: 2.7 A structure of the ATP-dependent chromatin remodeler Chd1 bou... -
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Basic information
Entry
Database: EMDB / ID: EMD-25480
Title
2.7 A structure of the ATP-dependent chromatin remodeler Chd1 bound to the nucleosome in a nucleotide-free state. This entry contains a better resolved DNA-binding domain
Map data
Sharpened 2.7A map with a negative bfactor (-17) in an orientation aligned to a common reference
Sample
Complex: Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state
Keywords
CHD1 / chromatin remodeling / ATPase / DBD / nucleosome / remodeling / transcription / DNA BINDING PROTEIN
Function / homology
Function and homology information
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01-GM084192
United States
Citation
Journal: Nat Struct Mol Biol / Year: 2022 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
Deposition
Nov 21, 2021
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Header (metadata) release
Mar 2, 2022
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Map release
Mar 2, 2022
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Update
Jan 17, 2024
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Current status
Jan 17, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
EMPIAR-10876 (Title: 2.3 A structure of the ATP-dependent chromatin remodeler Chd1 bound to the nucleosome in a nucleotide-free state 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])
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
Components
Complex: Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state
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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
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
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: FIELD EMISSION GUN
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