6UXW

SWI/SNF nucleosome complex with ADP-BeFx


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of SWI/SNF complex bound to a nucleosome.

Han, Y.Reyes, A.A.Malik, S.He, Y.

(2020) Nature 579: 452-455

  • DOI: https://doi.org/10.1038/s41586-020-2087-1
  • Primary Citation of Related Structures:  
    6UXV, 6UXW

  • PubMed Abstract: 

    The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair 1,2 . It hydrolyses ATP to remodel chromatin structure by sliding and evicting histone octamers 3-8 , creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodelling activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae SWI/SNF bound to a nucleosome, at near-atomic resolution. In the structure, the actin-related protein (Arp) module is sandwiched between the ATPase and the rest of the complex, with the Snf2 helicase-SANT associated (HSA) domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (also known as SMARCD or BAF60), Snf5 (also known as SMARCB1, BAF47 or INI1) and an asymmetric dimer of Swi3 (also known as SMARCC, BAF155 or BAF170). Another conserved subunit, Swi1 (also known as ARID1 or BAF250), resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure enables us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and to propose a model for how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation 9 .


  • Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2A [auth R],
E [auth V]
135Xenopus laevisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4B [auth S],
F [auth W]
102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1C [auth T],
G [auth X]
129Xenopus laevisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1D [auth U],
H [auth Y]
122Xenopus laevisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 7K [auth P]477Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein ARP9L [auth Q]467Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of Ty1 transposition protein 102M [auth Z]157Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription regulatory protein SNF2N [auth A]1,703Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF chromatin-remodeling complex subunit SWI1O [auth B]1,314Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF chromatin-remodeling complex subunit SNF5P [auth C]905Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF complex subunit SWI3Q [auth D],
R [auth E],
S [auth F],
T [auth G]
825Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription regulatory protein SNF12U [auth H]566Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription regulatory protein SNF6V [auth I]179Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown proteinAA [auth N],
BA [auth O],
W [auth J],
X [auth K],
Y [auth L]
67Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF global transcription activator complex subunit SWP82Z [auth M]83Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains LengthOrganismImage
601 sequence bottom strandI [auth a]185synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
601 sequence top strandJ [auth b]200synthetic construct
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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OA [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4

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CA [auth P]
DA [auth P]
EA [auth P]
FA [auth P]
GA [auth P]
CA [auth P],
DA [auth P],
EA [auth P],
FA [auth P],
GA [auth P],
HA [auth Q],
IA [auth Q],
JA [auth Q],
KA [auth Q],
LA [auth Q],
MA [auth Q],
NA [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
BEF
Query on BEF

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PA [auth A]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG
Query on MG

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QA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2020-03-18 
  • Deposition Author(s): He, Y., Han, Y.

Funding OrganizationLocationGrant Number
American Cancer SocietyUnited StatesIRG-15-173-21
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01 CA092584
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesU54CA193419

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Refinement description