6GEJ

Chromatin remodeller-nucleosome complex at 3.6 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 1.3 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: 10.1126/science.aat7716
  • Primary Citation of Related Structures:  
    6GEN, 6GEJ

  • 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 ...

    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. david.rueda@imperial.ac.uk d.wigley@imperial.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 72Z131Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3AB136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHT1YBR010WYBR0201HHT2SIN2YNL031CN2749
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4CD103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHF1YBR009CYBR0122HHF2YNL030WN2752
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A.1EF132Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTA1H2A1SPT11YDR225WYD9934.10
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B.1GH131Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTB1H2B1SPT12YDR224CYD9934.09C
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Helicase SWR1M1514Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWR1YDR334WD9651.6
EC: 3.6.4.12
Find proteins for Q05471 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-like protein ARP6R438Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP6YLR085CL2393L9449.13
Find proteins for Q12509 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 71S280Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS71SWC6YML041CYM8054.02C
Find proteins for Q03433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
RuvB-like protein 1TVX463Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RVB1TIH1TIP49AYDR190C
EC: 3.6.4.12
Find proteins for Q03940 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
RuvB-like protein 2UWY471Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RVB2TIH2TIP49BYPL235WP1060
EC: 3.6.4.12
Find proteins for Q12464 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (154-MER)I154synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (154-MER)J154synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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M, R, T, U, V, W, X, Y
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
BEF
Query on BEF

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M, R
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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M, R, U, V, W, X, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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
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 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-23
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Other