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 1.2 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: 10.1038/nature22036
  • Primary Citation of Related Structures:  

  • 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/su ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevis
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevis
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
129Xenopus laevis
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
122Xenopus laevis
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Transcription regulatory protein SNF2
O
735Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SNF2 (GAM1, RIC1, SWI2, TYE3)
EC: 3.6.4.-
Find proteins for P22082 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22082
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (167-MER)I167synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (167-MER)J167synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-04-26
    Type: Refinement description
  • Version 1.2: 2017-06-07
    Type: Database references