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: https://doi.org/10.1038/s41586-019-1029-2
  • Primary Citation of Related Structures:  
    5Z3L, 5Z3O, 5Z3U, 5Z3V, 6IY2, 6IY3

  • PubMed Abstract: 

    • 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 ...

    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: 

    Beijing Advanced Innovation Center for Structural Biology, Beijing, China. zhucheng_chen@tsinghua.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3
A, E
100Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
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Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4
B, F
88Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A
C, G
113Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg
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Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B
D, H
100Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032685mg
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription regulatory protein SNF2K [auth O]679Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNF2, GAM1, RIC1, SWI2, TYE3, YOR290C
EC: 3.6.4
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Find proteins for P22082 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (167-MER)I [auth J]147Mus musculus
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (147-MER)J [auth I]147Mus musculus
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
L [auth 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 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
China2017YFA0102900

Revision History  (Full details and data files)

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