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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 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 evictin ...

    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

    Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA. yuanhe@northwestern.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2RV135Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4SW102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1TX129Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1UY122Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 7P477Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP7SWP61YPR034WYP9367.14
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-like protein ARP9Q467Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP9SWP59YMR033WYM9973.07
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Regulator of Ty1 transposition protein 102Z157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RTT102YGR275WG9378
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription regulatory protein SNF2A1703Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNF2GAM1RIC1SWI2TYE3YOR290C
EC: 3.6.4
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
SWI/SNF chromatin-remodeling complex subunit SWI1B1314Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWI1ADR6GAM3YPL016WLPA1
Find proteins for P09547 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
SWI/SNF chromatin-remodeling complex subunit SNF5C905Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNF5SWI10TYE4YBR289WYBR2036
Find proteins for P18480 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
SWI/SNF complex subunit SWI3DEFG825Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWI3TYE2YJL176CJ0495
Find proteins for P32591 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription regulatory protein SNF12H566Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNF12SWP73YNR023WN3224
Find proteins for P53628 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription regulatory protein SNF6I179Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNF6
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown proteinJKLNO67Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
SWI/SNF global transcription activator complex subunit SWP82M83Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChainsLengthOrganismImage
601 sequence bottom stranda185synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
601 sequence top strandb200synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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A, P, Q
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
BEF
Query on BEF

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A
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-11-08 
  • 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 

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references