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
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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