8QYV

SWR1-hexasome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

Stabilization of the hexasome intermediate during histone exchange by yeast SWR1 complex.

Jalal, A.S.B.Girvan, P.Chua, E.Y.D.Liu, L.Wang, S.McCormack, E.A.Skehan, M.T.Knight, C.L.Rueda, D.S.Wigley, D.B.

(2024) Mol Cell 84: 3871

  • DOI: https://doi.org/10.1016/j.molcel.2024.08.015
  • Primary Citation of Related Structures:  
    8QYV, 8QZ0, 9FBW

  • PubMed Abstract: 

    The yeast SWR1 complex catalyzes the exchange of histone H2A/H2B dimers in nucleosomes with Htz1/H2B dimers. We use cryoelectron microscopy to determine the structure of an enzyme-bound hexasome intermediate in the reaction pathway of histone exchange, in which an H2A/H2B dimer has been extracted from a nucleosome prior to the insertion of a dimer comprising Htz1/H2B. The structure reveals a key role for the Swc5 subunit in stabilizing the unwrapping of DNA from the histone core of the hexasome. By engineering a crosslink between an Htz1/H2B dimer and its chaperone protein Chz1, we show that this blocks histone exchange by SWR1 but allows the incoming chaperone-dimer complex to insert into the hexasome. We use this reagent to trap an SWR1/hexasome complex with an incoming Htz1/H2B dimer that shows how the reaction progresses to the next step. Taken together the structures reveal insights into the mechanism of histone exchange by SWR1 complex.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
A, B
136Saccharomyces cerevisiae S288CMutation(s): 3 
Gene Names: HHT1
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
C, D
103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHF1
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.1132Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTA1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B.1F [auth G]131Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTB1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase SWR1I [auth M]1,514Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWR1
EC: 3.6.4.12
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
SWR1-complex protein 5J [auth P]303Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWC5
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein ARP6K [auth R]438Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP6
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 71L [auth S]280Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS71
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like protein 1M [auth T],
O [auth V],
Q [auth X]
463Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RVB1
EC: 3.6.4.12
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like protein 2N [auth U],
P [auth W],
R [auth Y]
471Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RVB2
EC: 3.6.4.12
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 72S [auth Z]795Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS72SWC2YDR485C
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (118-MER)G [auth I]118synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (118-MER)H [auth J]118synthetic construct
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

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BA [auth T]
DA [auth U]
FA [auth V]
HA [auth W]
JA [auth X]
BA [auth T],
DA [auth U],
FA [auth V],
HA [auth W],
JA [auth X],
LA [auth Y],
T [auth M],
W [auth R]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF (Subject of Investigation/LOI)
Query on BEF

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U [auth M],
X [auth R]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
ZN (Subject of Investigation/LOI)
Query on ZN

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AA [auth S],
Z [auth S]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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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],
V [auth M],
Y [auth R]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom095519/Z/11/Z & 209327/Z/17/Z
Cancer Research UKUnited KingdomC6913/A21608
Medical Research Council (MRC, United Kingdom)United KingdomMR/N009258/1 & MR/R009023/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary