6PWE

Cryo-EM structure of nucleosome core particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome.

Chittori, S.Hong, J.Bai, Y.Subramaniam, S.

(2019) Nucleic Acids Res 47: 9400-9409

  • DOI: 10.1093/nar/gkz670
  • Primary Citation of Related Structures:  
    6PWF, 6PWE

  • PubMed Abstract: 
  • ATP-dependent chromatin remodeling factors of SWI/SNF2 family including ISWI, SNF2, CHD1 and INO80 subfamilies share a conserved but functionally non-interchangeable ATPase domain. Here we report cryo-electron microscopy (cryo-EM) structures of the n ...

    ATP-dependent chromatin remodeling factors of SWI/SNF2 family including ISWI, SNF2, CHD1 and INO80 subfamilies share a conserved but functionally non-interchangeable ATPase domain. Here we report cryo-electron microscopy (cryo-EM) structures of the nucleosome bound to an ISWI fragment with deletion of the AutoN and HSS regions in nucleotide-free conditions and the free nucleosome at ∼ 4 Å resolution. In the bound conformation, the ATPase domain interacts with the super helical location 2 (SHL 2) of the nucleosomal DNA, with the N-terminal tail of H4 and with the α1 helix of H3. Density for other regions of ISWI is not observed, presumably due to disorder. Comparison with the structure of the free nucleosome reveals that although the histone core remains largely unchanged, remodeler binding causes perturbations in the nucleosomal DNA resulting in a bulge near the SHL2 site. Overall, the structure of the nucleotide-free ISWI-nucleosome complex is similar to the corresponding regions of the recently reported ADP bound ISWI-nucleosome structures, which are significantly different from that observed for the ADP-BeFx bound structure. Our findings are relevant to the initial step of ISWI binding to the nucleosome and provide additional insights into the nucleosome remodeling process driven by ISWI.


    Organizational Affiliation

    Frederick National Laboratory for Cancer Research, Frederick, MD, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3AE136Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P02299 (Drosophila melanogaster)
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Go to UniProtKB:  P02299
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF103Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P84040 (Drosophila melanogaster)
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Go to UniProtKB:  P84040
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2ACG124Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P84051 (Drosophila melanogaster)
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Go to UniProtKB:  P84051
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BDH123Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P02283 (Drosophila melanogaster)
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Go to UniProtKB:  P02283
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (147-MER)I147synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (147-MER)J147synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence