6GEN

Chromatin remodeller-nucleosome complex at 4.5 A resolution.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 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

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:  

  • 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.,Molecular Virology, Department of Medicine, Imperial College London, London W12 0NN, UK.,Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London W12 0NN, UK. david.rueda@imperial.ac.uk d.wigley@imperial.ac.uk.,Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London W12 0NN, UK.,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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 72
Z
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A, B
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HHT1, HHT2 (SIN2)
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P61830
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
C, D
103Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HHF1, HHF2
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02309
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2A.1
E, F
132Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HTA1 (H2A1, SPT11)
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04911
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2B.1
G, H
131Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HTB1 (H2B1, SPT12)
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02293
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Helicase SWR1
M
1514Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SWR1
EC: 3.6.4.12
Find proteins for Q05471 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05471
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Actin-like protein ARP6
R
438Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ARP6
Find proteins for Q12509 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12509
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 71
S
280Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VPS71 (SWC6)
Find proteins for Q03433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03433
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RuvB-like protein 1
T, V, X
463Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RVB1 (TIH1, TIP49A)
EC: 3.6.4.12
Find proteins for Q03940 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03940
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RuvB-like protein 2
U, W, Y
471Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RVB2 (TIH2, TIP49B)
EC: 3.6.4.12
Find proteins for Q12464 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12464
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (173-MER)I173synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (173-MER)J173synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

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

Download SDF File 
Download CCD File 
M, R, U, V, W, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
M, R
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
Z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references