9GD1

Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT.

Engeholm, M.Roske, J.J.Oberbeckmann, E.Dienemann, C.Lidschreiber, M.Cramer, P.Farnung, L.

(2024) Mol Cell 

  • DOI: https://doi.org/10.1016/j.molcel.2024.08.022
  • Primary Citation of Related Structures:  
    9GD0, 9GD1, 9GD2, 9GD3

  • PubMed Abstract: 

    To maintain the nucleosome organization of transcribed genes, ATP-dependent chromatin remodelers collaborate with histone chaperones. Here, we show that at the 5' ends of yeast genes, RNA polymerase II (RNAPII) generates hexasomes that occur directly adjacent to nucleosomes. The resulting hexasome-nucleosome complexes are then resolved by Chd1. We present two cryoelectron microscopy (cryo-EM) structures of Chd1 bound to a hexasome-nucleosome complex before and after restoration of the missing inner H2A/H2B dimer by FACT. Chd1 uniquely interacts with the complex, positioning its ATPase domain to shift the hexasome away from the nucleosome. In the absence of the inner H2A/H2B dimer, its DNA-binding domain (DBD) packs against the ATPase domain, suggesting an inhibited state. Restoration of the dimer by FACT triggers a rearrangement that displaces the DBD and stimulates Chd1 remodeling. Our results demonstrate how chromatin remodelers interact with a complex nucleosome assembly and suggest how Chd1 and FACT jointly support transcription by RNAPII.


  • Organizational Affiliation

    Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany. Electronic address: maik.engeholm@mpinat.mpg.de.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E, K, O
136Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F, L, P
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G, M
130Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H, N
123Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Chromo domain-containing protein 1Q [auth W]1,468Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CHD1YER164WSYGP-ORF4
EC: 3.6.4
UniProt
Find proteins for P32657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (261-MER)261synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (261-MER)261synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-09-25
    Changes: Data collection, Database references