6IY2

Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


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Literature

Mechanism of DNA translocation underlying chromatin remodelling by Snf2.

Li, M.Xia, X.Tian, Y.Jia, Q.Liu, X.Lu, Y.Li, M.Li, X.Chen, Z.

(2019) Nature 567: 409-413

  • DOI: 10.1038/s41586-019-1029-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme <sup>1,2 </sup>. Among the remodelling enzymes, Snf2 serves as the prototype to study the action of this pr ...

    Chromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme 1,2 . Among the remodelling enzymes, Snf2 serves as the prototype to study the action of this protein family. Snf2 and related enzymes share two conserved RecA-like lobes 3 , which by themselves are able to couple ATP hydrolysis to chromatin remodelling. The mechanism by which these enzymes couple ATP hydrolysis to translocate the nucleosome along the DNA remains unclear 2,4-8 . Here we report the structures of Saccharomyces cerevisiae Snf2 bound to the nucleosome in the presence of ADP and ADP-BeF x . Snf2 in the ADP-bound state adopts an open conformation similar to that in the apo state, and induces a one-base-pair DNA bulge at superhelix location 2 (SHL2), with the tracking strand showing greater distortion than the guide strand. The DNA distortion propagates to the proximal end, leading to staggered translocation of the two strands. The binding of ADP-BeF x triggers a closed conformation of the enzyme, resetting the nucleosome to a relaxed state. Snf2 shows altered interactions with the DNA in different nucleotide states, providing the structural basis for DNA translocation. Together, our findings suggest a fundamental mechanism for the DNA translocation that underlies chromatin remodelling.


    Organizational Affiliation

    Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,School of Life Science, Tsinghua University, Beijing, China. zhucheng_chen@tsinghua.edu.cn.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China. lixueming@mail.tsinghua.edu.cn.,MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, China.,Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China. mingli@iphy.ac.cn.,MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, China. zhucheng_chen@tsinghua.edu.cn.,Beijing Advanced Innovation Center for Structural Biology, Beijing, China. zhucheng_chen@tsinghua.edu.cn.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China. zhucheng_chen@tsinghua.edu.cn.,MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, China. lixueming@mail.tsinghua.edu.cn.,Beijing Advanced Innovation Center for Structural Biology, Beijing, China.,Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,School of Life Science, Tsinghua University, Beijing, China.,School of Life Science, Tsinghua University, Beijing, China. lixueming@mail.tsinghua.edu.cn.,Beijing Advanced Innovation Center for Structural Biology, Beijing, China. lixueming@mail.tsinghua.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A, E
100Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
88Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
113Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H
100Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Transcription regulatory protein SNF2
O
679Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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)J147Mus musculus
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (147-MER)I147Mus musculus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
O
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China2017YFA0102900

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release