6GEN

Chromatin remodeller-nucleosome complex at 4.5 A resolution.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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

Structure and dynamics of the yeast SWR1-nucleosome complex.

Willhoft, O., Ghoneim, M., Lin, C.L., Chua, E.Y.D., Wilkinson, M., Chaban, Y., Ayala, R., McCormack, E.A., Ocloo, L., Rueda, D.S., Wigley, D.B.

(2018) Science 362

  • DOI: https://doi.org/10.1126/science.aat7716
  • Primary Citation of Related Structures:  
    6GEJ, 6GEN

  • PubMed Abstract: 

    The yeast SWR1 complex exchanges histone H2A in nucleosomes with Htz1 (H2A.Z in humans). The cryo-electron microscopy structure of the SWR1 complex bound to a nucleosome at 3.6-angstrom resolution reveals details of the intricate interactions between components of the SWR1 complex and its nucleosome substrate. Interactions between the Swr1 motor domains and the DNA wrap at superhelical location 2 distort the DNA, causing a bulge with concomitant translocation of the DNA by one base pair, coupled to conformational changes of the histone core. Furthermore, partial unwrapping of the DNA from the histone core takes place upon binding of nucleosomes to SWR1 complex. The unwrapping, as monitored by single-molecule data, is stabilized and has its dynamics altered by adenosine triphosphate binding but does not require hydrolysis.

    • Organizational Affiliation: 

    Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 72A [auth Z]131Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3B [auth A],
C [auth B]		136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth C],
E [auth D]		103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.1F [auth E],
G [auth F]		132Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTA1, H2A1, SPT11, YDR225W, YD9934.10
UniProt
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B.1H [auth G],
I [auth H]		131Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTB1, H2B1, SPT12, YDR224C, YD9934.09C
UniProt
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase SWR1L [auth M]1,514Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWR1, YDR334W, D9651.6
EC: 3.6.4.12
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein ARP6M [auth R]438Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP6, YLR085C, L2393, L9449.13
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 71N [auth S]280Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS71, SWC6, YML041C, YM8054.02C
UniProt
Find proteins for Q03433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like protein 1O [auth T],
Q [auth V],
S [auth X]		463Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RVB1, TIH1, TIP49A, YDR190C
EC: 3.6.4.12
UniProt
Find proteins for Q03940 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like protein 2P [auth U],
R [auth W],
T [auth Y]		471Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RVB2, TIH2, TIP49B, YPL235W, P1060
EC: 3.6.4.12
UniProt
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (173-MER)J [auth I]173synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (173-MER)K [auth J]173synthetic 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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CA [auth T]
EA [auth U]
GA [auth V]
IA [auth W]
KA [auth X]
CA [auth T],
EA [auth U],
GA [auth V],
IA [auth W],
KA [auth X],
MA [auth Y],
U [auth M],
X [auth R]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF
Query on BEF
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V [auth M],
Y [auth R]		BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
ZN
Query on ZN
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AA [auth S],
BA [auth S]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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DA [auth U]
FA [auth U]
HA [auth V]
JA [auth W]
LA [auth Y]
DA [auth U],
FA [auth U],
HA [auth V],
JA [auth W],
LA [auth Y],
NA [auth Y],
W [auth M],
Z [auth R]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1.0

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom095519/Z/11/Z
Wellcome TrustUnited Kingdom209327/Z/17/Z
Cancer Research UKUnited KingdomC6913/A21608
Medical Research Council (United Kingdom)United KingdomMR/N009258/1
Medical Research Council (United Kingdom)United KingdomMR/R009023/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other