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- PDB-30gf: Structural characterisation of chromatin remodelling intermediate... -

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Basic information

Entry
Database: PDB / ID: 30gf
TitleStructural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.
Components
  • (DNA (154-MER)) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3.2
  • Histone H4
KeywordsGENE REGULATION / Nucleosome / Remodelling enzyme
Function / homologyDNA / DNA (> 10) / DNA (> 100)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsSundaramoorthy, R. / Hughes, A. / Owen-hughes, T.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Elife / Year: 2025
Title: Structural characterisation of chromatin remodelling intermediates supports linker DNA-dependent product inhibition as a mechanism for nucleosome spacing.
Authors: Amanda L Hughes / Ramasubramanian Sundaramoorthy / Tom Owen-Hughes /
Abstract: Previously, we showed that Chd1 chromatin remodelling enzyme associates with nucleosomes oriented towards the longer linker (Sundaramoorthy et al., 2018) (1). Here, we report a series of structures ...Previously, we showed that Chd1 chromatin remodelling enzyme associates with nucleosomes oriented towards the longer linker (Sundaramoorthy et al., 2018) (1). Here, we report a series of structures of Chd1 bound to nucleosomes during ongoing ATP-dependent repositioning. Combining these with biochemical experiments and existing literature, we propose a model in which Chd1 first associates oriented to sample putative entry DNA. In an ATP-dependent reaction, the enzyme then redistributes to the opposite side of the nucleosome, where it subsequently adopts a conformation productive for DNA translocation. Once this active complex extends the nascent exit linker to approximately 15 bp, it is sensed by the Chd1 DNA binding domain, resulting in conversion to a product-inhibited state. These observations provide a mechanistic basis for the action of a molecular ruler element in nucleosome spacing.
History
DepositionApr 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (154-MER)
J: DNA (154-MER)


Theoretical massNumber of molelcules
Total (without water)210,15010
Polymers210,15010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2


Mass: 15403.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: structural protein
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
#2: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Structural protein
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
#3: Protein Histone H2A


Mass: 13993.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: structural protein
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
#4: Protein Histone H2B


Mass: 13965.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: structural protein
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (154-MER)


Mass: 50080.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DNA / Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#6: DNA chain DNA (154-MER)


Mass: 50557.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DNA / Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Nucleosome-Chd1 complex / Type: COMPLEX / Details: Chd1 remodeller bound to Nucleosome / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 20mM HEPES, 120mM Nacl pH 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1120 mMSodium chlorideNaCl1
220 mMHEPESHEPES1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified Nucleosome-Chd1 complex
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Vitrification carried out in climate chamber with 100% humidity

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 81000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1800 nm / Calibrated defocus min: 1800 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K
Image recordingAverage exposure time: 10 sec. / Electron dose: 46 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2562

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.17particle selection
4cryoSPARC4.5.3CTF correction
7PHENIX1.21_5207model fitting
8ISOLDE1.1model fitting
9Coot0.98.53model fitting
11cryoSPARC4.5.3initial Euler assignment
12cryoSPARC4.5.3final Euler assignment
13cryoSPARC4.5.3classification
14cryoSPARC4.5.33D reconstruction
15PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 2700000
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 180 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13LZ0

3lz0

13LZ01PDBexperimental model
26FTX

6ftx

16FTX2PDBexperimental model
37TN2

7tn2

17TN23PDBexperimental model
RefinementHighest resolution: 4.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0113015
ELECTRON MICROSCOPYf_angle_d1.22918903
ELECTRON MICROSCOPYf_dihedral_angle_d27.4485624
ELECTRON MICROSCOPYf_chiral_restr0.0952149
ELECTRON MICROSCOPYf_plane_restr0.011327

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