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- PDB-9n6h: 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex -

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Basic information

Entry
Database: PDB / ID: 9n6h
Title2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex
Components
  • Chromo domain-containing protein 1
  • DNA Lagging Strand
  • DNA Tracking Strand
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / chromatin / CHD1 / remodeler / ATP-dependent chromatin remodeler / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / SLIK (SAGA-like) complex / rDNA binding / 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 / SLIK (SAGA-like) complex / rDNA binding / 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 / nucleosome / heterochromatin formation / 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
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
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B 1.1 / Chromo domain-containing protein 1 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciessynthetic construct (others)
Xenopus laevis (African clawed frog)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsNodelman, I.M. / Folkwein, H.J. / Armache, J.-P. / Bowman, G.D.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA Tracking Strand
J: DNA Lagging Strand
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
K: Chromo domain-containing protein 1
E: Histone H3
A: Histone H3


Theoretical massNumber of molelcules
Total (without water)283,83911
Polymers283,83911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 2 types, 2 molecules IJ

#1: DNA chain DNA Tracking Strand


Mass: 49127.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA Lagging Strand


Mass: 49656.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Protein , 5 types, 9 molecules BFCGDHKEA

#3: Protein Histone H4


Mass: 10061.849 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#4: Protein Histone H2A


Mass: 12082.128 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#5: Protein Histone H2B 1.1 / H2B1.1


Mass: 10494.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#6: Protein Chromo domain-containing protein 1 / ATP-dependent helicase CHD1


Mass: 96773.930 Da / Num. of mol.: 1 / Fragment: residues 122-956 / Mutation: L886G, L889G, L891G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CHD1, YER164W, SYGP-ORF4 / Production host: Escherichia coli (E. coli)
References: UniProt: P32657, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#7: Protein Histone H3


Mass: 11502.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065, LOC108703785, LOC121398067 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1

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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: Complex between nucleosome and CHD1 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 450 kDa/nm / Experimental value: NO
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 defocus max: 2200 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2PHENIX1.21_5207model refinement
3EPU3.31image acquisition
5cryoSPARC4.6.2CTF correction
10cryoSPARC4.6.2initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.6.2classification
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 15463267
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 297046 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT

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