5O9G

Structure of nucleosome-Chd1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nucleosome-Chd1 structure and implications for chromatin remodelling.

Farnung, L.Vos, S.M.Wigge, C.Cramer, P.

(2017) Nature 550: 539-542

  • DOI: 10.1038/nature24046

  • PubMed Abstract: 
  • Chromatin-remodelling factors change nucleosome positioning and facilitate DNA transcription, replication, and repair. The conserved remodelling factor chromodomain-helicase-DNA binding protein 1(Chd1) can shift nucleosomes and induce regular nucleos ...

    Chromatin-remodelling factors change nucleosome positioning and facilitate DNA transcription, replication, and repair. The conserved remodelling factor chromodomain-helicase-DNA binding protein 1(Chd1) can shift nucleosomes and induce regular nucleosome spacing. Chd1 is required for the passage of RNA polymerase IIthrough nucleosomes and for cellular pluripotency. Chd1 contains the DNA-binding domains SANT and SLIDE, a bilobal motor domain that hydrolyses ATP, and a regulatory double chromodomain. Here we report the cryo-electron microscopy structure of Chd1 from the yeast Saccharomyces cerevisiae bound to a nucleosome at a resolution of 4.8 Å. Chd1 detaches two turns of DNA from the histone octamer and binds between the two DNA gyres in a state poised for catalysis. The SANT and SLIDE domains contact detached DNA around superhelical location (SHL) -7 of the first DNA gyre. The ATPase motor binds the second DNA gyre at SHL +2 and is anchored to the N-terminal tail of histone H4, as seen in a recent nucleosome-Snf2 ATPase structure. Comparisons with published results reveal that the double chromodomain swings towards nucleosomal DNA at SHL +1, resulting in ATPase closure. The ATPase can then promote translocation of DNA towards the nucleosome dyad, thereby loosening the first DNA gyre and remodelling the nucleosome. Translocation may involve ratcheting of the two lobes of the ATPase, which is trapped in a pre- or post-translocation state in the absence or presence, respectively, of transition state-mimicking compounds.


    Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
136Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
130Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D
123Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
H
122Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Chromo domain-containing protein 1
W
1468Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CHD1
EC: 3.6.4.-
Find proteins for P32657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CHD1
Go to UniProtKB:  P32657
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (162-MER)I208synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (162-MER)J208synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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W
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
BEF
Query on BEF

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Download CCD File 
W
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Germany--

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references
  • Version 1.2: 2017-11-01
    Type: Database references