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- EMDB-53595: Structural characterisation of chromatin remodelling intermediate... -

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Basic information

Entry
Database: EMDB / ID: EMD-53595
TitleStructural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.
Map data
Sample
  • Complex: Nucleosome-Chd1 complex
    • DNA: DNA (160-MER)
    • DNA: DNA (160-MER)
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Chromo domain-containing protein 1
KeywordsNucleosome / Remodelling enzyme / GENE REGULATION
Function / homology
Function and homology information


regulation of transcriptional start site selection at RNA polymerase II promoter / nucleolar chromatin / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / SAGA complex ...regulation of transcriptional start site selection at RNA polymerase II promoter / nucleolar chromatin / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / SAGA complex / sister chromatid cohesion / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / : / ATP-dependent activity, acting on DNA / transcription elongation by RNA polymerase II / helicase activity / double-strand break repair via homologous recombination / chromatin DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / heterochromatin formation / 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 / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain ...Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Chromo domain-containing protein 1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / synthetic construct (others) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSundaramoorthy R / Hughes A / Owen-hughes TA
Funding support United Kingdom, 1 items
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 of ...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 nascent exit linker to approximately 15bp, 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
DepositionMay 9, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53595.png

Downloads & links

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Map

FileDownload / File: emd_53595.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.55 Å/pix.
x 560 pix.
= 308. Å		0.55 Å/pix.
x 560 pix.
= 308. Å		0.55 Å/pix.
x 560 pix.
= 308. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.55 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0018255403 - 2.5066898
Average (Standard dev.)0.0017526784 (±0.032106508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53595_msk_1.map
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Additional map: #1

Fileemd_53595_additional_1.map
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Half map: #2

Fileemd_53595_half_map_1.map
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Half map: #1

Fileemd_53595_half_map_2.map
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Sample components

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Entire : Nucleosome-Chd1 complex

EntireName: Nucleosome-Chd1 complex
Components
  • Complex: Nucleosome-Chd1 complex
    • DNA: DNA (160-MER)
    • DNA: DNA (160-MER)
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Chromo domain-containing protein 1

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Supramolecule #1: Nucleosome-Chd1 complex

SupramoleculeName: Nucleosome-Chd1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Chd1 remodeller bound to Nucleosome
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: DNA (160-MER)

MacromoleculeName: DNA (160-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 49.158293 KDa
SequenceString: (DC)(DC)(DC)(DT)(DA)(DT)(DA)(DC)(DG)(DC) (DG)(DG)(DG)(DC)(DG)(DC)(DA)(DC)(DT)(DG) (DC)(DA)(DG)(DA)(DA)(DG)(DC)(DT)(DT) (DG)(DG)(DT)(DC)(DC)(DC)(DG)(DG)(DG)(DG) (DC) (DC)(DG)(DC)(DT)(DC)(DA) ...String:
(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DC)(DG)(DC) (DG)(DG)(DG)(DC)(DG)(DC)(DA)(DC)(DT)(DG) (DC)(DA)(DG)(DA)(DA)(DG)(DC)(DT)(DT) (DG)(DG)(DT)(DC)(DC)(DC)(DG)(DG)(DG)(DG) (DC) (DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DC) (DA)(DA) (DG)(DC)(DT)(DC)(DT)(DA)(DG) (DA)(DT)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DT)(DC)(DG) (DA)(DA)(DC)(DG)(DT)(DA) (DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC) (DC)(DC)(DC)(DG) (DC)(DG)(DT)(DT)(DT) (DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA) (DG)(DG)(DG)(DG)(DA) (DT)(DT)(DA)(DC) (DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DG)(DC) (DA)(DC)(DG) (DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DC)(DA)(DT)(DC)

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Macromolecule #2: DNA (160-MER)

MacromoleculeName: DNA (160-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 49.625605 KDa
SequenceString: (DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA) (DT)(DC)(DC)(DC)(DC)(DT) ...String:
(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA) (DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG) (DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA) (DC)(DG) (DC)(DG)(DG)(DG)(DG)(DG)(DA) (DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC) (DG)(DT)(DT) (DC)(DG)(DA)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DA)(DT)(DC)(DT)(DA) (DG)(DA)(DG)(DC) (DT)(DT)(DG)(DC)(DT) (DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG) (DG)(DC)(DC)(DC) (DC)(DG)(DG)(DG)(DA)(DC)(DC)(DA)(DA)(DG) (DC)(DT)(DT)(DC)(DT)(DG) (DC)(DA)(DG) (DT)(DG)(DC)(DG)(DC)(DC)(DC)(DG)(DC)(DG) (DT)(DA)(DT)(DA)(DG)(DG)(DG)

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Macromolecule #3: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.421101 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #5: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.993295 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG GVTIAQGGVL PNIQSVLLPK KTESAKSAKS K

UniProtKB: Histone H2A type 1

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Macromolecule #6: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.965265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Chromo domain-containing protein 1

MacromoleculeName: Chromo domain-containing protein 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 168.365422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AAKDISTEVL QNPELYGLRR SHRAAAHQQN YFNDSDDEDD EDNIKQSRRK RMTTIEDDED EFEDEEGEED SGEDEDEEDF EEDDDYYGS PIKQNRSKPK SRTKSKSKSK PKSQSEKQST VKIPTRFSNR QNKTVNYNID YSDDDLLESE DDYGSEEALS E ENVHEASA ...String:
AAKDISTEVL QNPELYGLRR SHRAAAHQQN YFNDSDDEDD EDNIKQSRRK RMTTIEDDED EFEDEEGEED SGEDEDEEDF EEDDDYYGS PIKQNRSKPK SRTKSKSKSK PKSQSEKQST VKIPTRFSNR QNKTVNYNID YSDDDLLESE DDYGSEEALS E ENVHEASA NPQPEDFHGI DIVINHRLKT SLEEGKVLEK TVPDLNNCKE NYEFLIKWTD ESHLHNTWET YESIGQVRGL KR LDNYCKQ FIIEDQQVRL DPYVTAEDIE IMDMERERRL DEFEEFHVPE RIIDSQRASL EDGTSQLQYL VKWRRLNYDE ATW ENATDI VKLAPEQVKH FQNRENSKIL PQYSSNYTSQ RPRFEKLSVQ PPFIKGGELR DFQLTGINWM AFLWSKGDNG ILAD EMGLG KTVQTVAFIS WLIFARRQNG PHIIVVPLST MPAWLDTFEK WAPDLNCICY MGNQKSRDTI REYEFYTNPR AKGKK TMKF NVLLTTYEYI LKDRAELGSI KWQFMAVDEA HRLKNAESSL YESLNSFKVA NRMLITGTPL QNNIKELAAL VNFLMP GRF TIDQEIDFEN QDEEQEEYIH DLHRRIQPFI LRRLKKDVEK SLPSKTERIL RVELSDVQTE YYKNILTKNY SALTAGA KG GHFSLLNIMN ELKKASNHPY LFDNAEERVL QKFGDGKMTR ENVLRGLIMS SGKMVLLDQL LTRLKKDGHR VLIFSQMV R MLDILGDYLS IKGINFQRLD GTVPSAQRRI SIDHFNSPDS NDFVFLLSTR AGGLGINLMT ADTVVIFDSD WNPQADLQA MARAHRIGQK NHVMVYRLVS KDTVEEEVLE RARKKMILEY AIISLGVTDG NKYTKKNEPN AGELSAILKF GAGNMFTATD NQKKLEDLN LDDVLNHAED HVTTPDLGES HLGGEEFLKQ FEVTDYKADI DWDDIIPEEE LKKLQDEEQK RKDEEYVKEQ L EMMNRRDN ALKKIKNSVN GDGTAANSDS DDDSTSRSSR RRARANDMDS IGESEVRALY KAILKFGNLK EILDELIADG TL PVKSFEK YGETYDEMME AAKDCVHEEE KNRKEILEKL EKHATAYRAK LKSGEIKAEN QPKDNPLTRL SLKKREKKAV LFN FKGVKS LNAESLLSRV EDLKYLKNLI NSNYKDDPLK FSLGNNTPKP VQNWSSNWTK EEDEKLLIGV FKYGYGSWTQ IRDD PFLGI TDKIFLNEVH NPVAKKSASS SDTTPTPSKK GKGITGSSKK VPGAIHLGRR VDYLLSFLRG GLNTKSPSAD IGSKK LPTG PSKKRQRKPA NHSKSMTPEI TSSEPANGPP SKRMKALPKG PAALINNTRL SPNSPTPPLK SKVSRDNGTR QSSNPS SGS AHEKEYDSMD EEDCRHTMSA IRTSLKRLRR GGKSLDRKEW AKILKTELTT IGNHIESQKG SSRKASPEKY RKHLWSY SA NFWPADVKST KLMAMYDKIT ESQKK

UniProtKB: Chromo domain-containing protein 1

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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
Component:
ConcentrationFormulaName
120.0 mMNaclSodium chloride
20.0 mMHepesHepes

Details: 20mM Hepes, 120mM Nacl
GridModel: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0001 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrified carried out in climate chamber with 100% humidity.
DetailsPurified Nucleosome-Chd1 complex.

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2562 / Average exposure time: 10.0 sec. / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.2 µm / Calibrated defocus min: 1.8 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000
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: 2700000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3lz0

Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 110000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 4 / Avg.num./class: 100000 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3lz0

source_name: PDB, initial_model_type: experimental model

6ftx

source_name: PDB, initial_model_type: experimental model

7tn2

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 180 / Target criteria: cross-correlation
Output model

PDB-9r5s:
Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.

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