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- EMDB-49060: 2.37 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome reconstruc... -

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Basic information

Entry
Database: EMDB / ID: EMD-49060
Title2.37 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome reconstructruction. Combined 1:1 and 2:1 complexes
Map dataUnsharpened map
Sample
  • Complex: Complex between nucleosome and CHD1
    • Complex: CHD1
    • Complex: histone proteins
    • Complex: DNA
Keywordschromatin / CHD1 / remodeler / ATP-dependent chromatin remodeler / DNA BINDING PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsNodelman IM / Folkwein HJ / Armache J-P / Bowman GD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM084192 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: A competitive regulatory mechanism of the Chd1 remodeler is integral to distorting nucleosomal DNA.
Authors: Ilana M Nodelman / Heather J Folkwein / Wesley S Glime / Jean-Paul Armache / Gregory D Bowman /
Abstract: The Chd1 chromatin remodeler repositions nucleosomes into evenly spaced arrays, a characteristic of most eukaryotic genes. Here we show that the yeast Chd1 remodeler requires two activating segments ...The Chd1 chromatin remodeler repositions nucleosomes into evenly spaced arrays, a characteristic of most eukaryotic genes. Here we show that the yeast Chd1 remodeler requires two activating segments to distort nucleosomal DNA into an A-form-like conformation, a critical first step in nucleosome sliding. As shown by cryo-electron microscopy, these two activating segments together pack against the ATPase motor, where they are poised to stabilize the central ATPase cleft. These activating elements contact the ATPase at locations that are incompatible with binding of NegC, an autoinhibitory segment located between the two activators. NegC inhibits sliding by antagonizing the activators through steric competition and constraining activator placement, giving rise to directional nucleosome sliding. Given that activator reinforcement of the ATPase cleft is needed for DNA distortion, this first step in remodeling appears to provide a natural checkpoint for regulation of chromatin remodeler activity.
History
DepositionFeb 5, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49060.png

Downloads & links

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Map

FileDownload / File: emd_49060.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336.128 Å		1.05 Å/pix.
x 320 pix.
= 336.128 Å		1.05 Å/pix.
x 320 pix.
= 336.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0504 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum0.0 - 1.6657796
Average (Standard dev.)0.0033260963 (±0.02740694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: uto-sharpened map with bfactor = -52.1

Fileemd_49060_additional_1.map
Annotationuto-sharpened map with bfactor = -52.1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_49060_half_map_1.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_49060_half_map_2.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between nucleosome and CHD1

EntireName: Complex between nucleosome and CHD1
Components
  • Complex: Complex between nucleosome and CHD1
    • Complex: CHD1
    • Complex: histone proteins
    • Complex: DNA

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Supramolecule #1: Complex between nucleosome and CHD1

SupramoleculeName: Complex between nucleosome and CHD1 / type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 450 kDa/nm

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Supramolecule #2: CHD1

SupramoleculeName: CHD1 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: histone proteins

SupramoleculeName: histone proteins / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen 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

Particle selectionNumber selected: 15463267
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 710376
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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