8D4Y

C-terminal SANT-SLIDE domain of human Chromodomain-helicase-DNA-binding protein 4 (CHD4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families.

Zhong, Y.Moghaddas Sani, H.Paudel, B.P.Low, J.K.K.Silva, A.P.G.Mueller, S.Deshpande, C.Panjikar, S.Reid, X.J.Bedward, M.J.van Oijen, A.M.Mackay, J.P.

(2022) Nat Commun 13: 7524-7524

  • DOI: https://doi.org/10.1038/s41467-022-35002-0
  • Primary Citation of Related Structures:  
    8D4Y

  • PubMed Abstract: 

    CHD4 is an essential, widely conserved ATP-dependent translocase that is also a broad tumour dependency. In common with other SF2-family chromatin remodelling enzymes, it alters chromatin accessibility by repositioning histone octamers. Besides the helicase and adjacent tandem chromodomains and PHD domains, CHD4 features 1000 residues of N- and C-terminal sequence with unknown structure and function. We demonstrate that these regions regulate CHD4 activity through different mechanisms. An N-terminal intrinsically disordered region (IDR) promotes remodelling integrity in a manner that depends on the composition but not sequence of the IDR. The C-terminal region harbours an auto-inhibitory region that contacts the helicase domain. Auto-inhibition is relieved by a previously unrecognized C-terminal SANT-SLIDE domain split by ~150 residues of disordered sequence, most likely by binding of this domain to substrate DNA. Our data shed light on CHD4 regulation and reveal strong mechanistic commonality between CHD family members, as well as with ISWI-family remodellers.


  • Organizational Affiliation

    School of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW, 2006, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromodomain-helicase-DNA-binding protein 4
A, B
431Homo sapiensMutation(s): 0 
Gene Names: CHD4
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q14839 (Homo sapiens)
Explore Q14839 
Go to UniProtKB:  Q14839
PHAROS:  Q14839
GTEx:  ENSG00000111642 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14839
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.432α = 90
b = 66.665β = 100.77
c = 99.37γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
Auto-Rickshawphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description