6FTX

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 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 of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome.

Sundaramoorthy, R.Hughes, A.L.El-Mkami, H.Norman, D.G.Ferreira, H.Owen-Hughes, T.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.35720
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the <i>Saccharomyces cerevisiae </i> Chd1 protein eng ...

    ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.


    Organizational Affiliation

    Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Nucleic Acids Structure Research Group, University of Dundee, Dundee, United Kingdom.,School of Biology, University of St Andrews, St Andrews, United Kingdom.,School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A
97Petromyzon marinusMutation(s): 0 
Find proteins for S4RAZ3 (Petromyzon marinus)
Go to UniProtKB:  S4RAZ3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G
130Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H
126Xenopus tropicalisMutation(s): 0 
Gene Names: hist2h2bf (LOC108648866)
Find proteins for Q28D68 (Xenopus tropicalis)
Go to UniProtKB:  Q28D68
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3C
E
110Xenopus laevisMutation(s): 0 
Gene Names: h3f3c
Find proteins for P02302 (Xenopus laevis)
Go to UniProtKB:  P02302
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
N, O
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Chromatin-remodeling ATPase
W
878Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CHD1
EC: 3.6.4.-
Find proteins for P32657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CHD1
Go to UniProtKB:  P32657
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (159-MER)I159synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (160-MER)J160synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

Download SDF File 
Download CCD File 
W
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-22
    Type: Data collection, Database references
  • Version 1.2: 2018-10-17
    Type: Data collection, Refinement description, Structure summary