6RYR

Nucleosome-CHD4 complex structure (single CHD4 copy)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Nucleosome-CHD4 chromatin remodeller structure maps human disease mutations.

Farnung, L.Ochmann, M.Cramer, P.

(2020) Elife 9

  • DOI: 10.7554/eLife.56178
  • Primary Citation of Related Structures:  
    6RYU, 6RYR

  • PubMed Abstract: 
  • Chromatin remodeling plays important roles in gene regulation during development, differentiation and in disease. The chromatin remodeling enzyme CHD4 is a component of the NuRD and ChAHP complexes that are involved in gene repression. Here, we repor ...

    Chromatin remodeling plays important roles in gene regulation during development, differentiation and in disease. The chromatin remodeling enzyme CHD4 is a component of the NuRD and ChAHP complexes that are involved in gene repression. Here, we report the cryo-electron microscopy (cryo-EM) structure of Homo sapiens CHD4 engaged with a nucleosome core particle in the presence of the non-hydrolysable ATP analogue AMP-PNP at an overall resolution of 3.1 Å. The ATPase motor of CHD4 binds and distorts nucleosomal DNA at superhelical location (SHL) +2, supporting the 'twist defect' model of chromatin remodeling. CHD4 does not induce unwrapping of terminal DNA, in contrast to its homologue Chd1, which functions in gene activation. Our structure also maps CHD4 mutations that are associated with human cancer or the intellectual disability disorder Sifrim-Hitz-Weiss syndrome.


    Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2AE136Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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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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Go to UniProtKB:  P62799
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1CG130Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
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Go to UniProtKB:  P06897
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1DH123Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
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Go to UniProtKB:  P02281
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Chromodomain-helicase-DNA-binding protein 4,Chromodomain-helicase-DNA-binding protein 4,Chromodomain-helicase-DNA-binding protein 4W1927Homo sapiensMutation(s): 0 
Gene Names: CHD4
EC: 3.6.4.12
Find proteins for Q14839 (Homo sapiens)
Explore Q14839 
Go to UniProtKB:  Q14839
NIH Common Fund Data Resources
PHAROS  Q14839
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (149-MER)I149synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (149-MER)J149synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

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PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

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

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W
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany693023
German Research Foundation (DFG)GermanySFB1064
German Research Foundation (DFG)GermanySFB860
Volkswagen FoundationGermany--

Revision History 

  • Version 1.0: 2020-07-15
    Type: Initial release