5X0Y

Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure.

Liu, X.Li, M.Xia, X.Li, X.Chen, Z.

(2017) Nature 544: 440-445

  • DOI: https://doi.org/10.1038/nature22036
  • Primary Citation of Related Structures:  
    5X0X, 5X0Y

  • PubMed Abstract: 

    Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron microscopy structure of chromatin remodeller Switch/sucrose non-fermentable (SWI2/SNF2) from Saccharomyces cerevisiae bound to the nucleosome. The structure shows that the two core domains of Snf2 are realigned upon nucleosome binding, suggesting activation of the enzyme. The core domains contact each other through two induced Brace helices, which are crucial for coupling ATP hydrolysis to chromatin remodelling. Snf2 binds to the phosphate backbones of one DNA gyre of the nucleosome mainly through its helicase motifs within the major domain cleft, suggesting a conserved mechanism of substrate engagement across different remodellers. Snf2 contacts the second DNA gyre via a positively charged surface, providing a mechanism to anchor the remodeller at a fixed position of the nucleosome. Snf2 locally deforms nucleosomal DNA at the site of binding, priming the substrate for the remodelling reaction. Together, these findings provide mechanistic insights into chromatin remodelling.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
135Xenopus 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
102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
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
122Xenopus 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
Transcription regulatory protein SNF2K [auth O]735Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNF2GAM1RIC1SWI2TYE3YOR290C
EC: 3.6.4
UniProt
Find proteins for P22082 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP22082
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (167-MER)167synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (167-MER)167synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Refinement description
  • Version 1.2: 2017-06-07
    Changes: Database references
  • Version 1.3: 2019-10-09
    Changes: Data collection, Other, Structure summary
  • Version 1.4: 2024-03-27
    Changes: Data collection, Database references