9N6H | pdb_00009n6h

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A competitive regulatory mechanism of the Chd1 remodeler is integral to distorting nucleosomal DNA.

Nodelman, I.M.Folkwein, H.J.Glime, W.S.Armache, J.P.Bowman, G.D.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-025-01556-y
  • Primary Citation of Related Structures:  
    9N6H, 9N6I, 9N6K

  • PubMed 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 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.


  • Organizational Affiliation

    Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4C [auth B],
F
88Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AD [auth C],
G
110Xenopus laevisMutation(s): 0 
Gene Names: LOC494591h2ac14.Lhist1h2ajhist1h2aj.L
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
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UniProt GroupQ6AZJ8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1E [auth D],
H
94Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Chromo domain-containing protein 1I [auth K]835Saccharomyces cerevisiaeMutation(s): 3 
Gene Names: CHD1YER164WSYGP-ORF4
EC: 3.6.4
UniProt
Find proteins for P32657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP32657
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3J [auth E],
K [auth A]
98Xenopus laevisMutation(s): 0 
Gene Names: LOC121398065LOC108703785LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis)
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UniProt GroupA0A310TTQ1
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA Tracking StrandA [auth I]160synthetic construct
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA Lagging StrandB [auth J]160synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC4.6.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM084192

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release