6G0L

Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.5 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:  
    6FTX, 6G0L

  • 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 Saccharomyces cerevisiae 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.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3AE136Xenopus laevisMutation(s): 0 
Gene Names: hist1h3gH3lh3c8.Sh3c8
Find proteins for Q92133 (Xenopus laevis)
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1C130Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4DH126Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18028549mg
Find proteins for A0A1L8G0X3 (Xenopus laevis)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1G130Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
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  • Reference Sequence
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Chromo domain-containing protein 1MW1468Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CHD1YER164WSYGP-ORF4
EC: 3.6.4
Find proteins for P32657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (176-MER)I176synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (177-MER)J177synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.0 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 Kingdom--

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-12
    Changes: Data collection, Data processing
  • Version 1.3: 2018-10-03
    Changes: Data collection, Refinement description
  • Version 1.4: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations