6IPU

Human nucleosome core particle containing 145 bp of DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

PARP1 exhibits enhanced association and catalytic efficiency with gamma H2A.X-nucleosome.

Sharma, D.De Falco, L.Padavattan, S.Rao, C.Geifman-Shochat, S.Liu, C.F.Davey, C.A.

(2019) Nat Commun 10: 5751-5751

  • DOI: 10.1038/s41467-019-13641-0
  • Primary Citation of Related Structures:  
    6K1I, 6K1K, 6K1J, 6JXD, 6IPU

  • PubMed Abstract: 
  • The poly(ADP-ribose) polymerase, PARP1, plays a key role in maintaining genomic integrity by detecting DNA damage and mediating repair. γH2A.X is the primary histone marker for DNA double-strand breaks and PARP1 localizes to H2A.X-enriched chromatin damage sites, but the basis for this association is not clear ...

    The poly(ADP-ribose) polymerase, PARP1, plays a key role in maintaining genomic integrity by detecting DNA damage and mediating repair. γH2A.X is the primary histone marker for DNA double-strand breaks and PARP1 localizes to H2A.X-enriched chromatin damage sites, but the basis for this association is not clear. We characterize the kinetics of PARP1 binding to a variety of nucleosomes harbouring DNA double-strand breaks, which reveal that PARP1 associates faster with (γ)H2A.X- versus H2A-nucleosomes, resulting in a higher affinity for the former, which is maximal for γH2A.X-nucleosome that is also the activator eliciting the greatest poly-ADP-ribosylation catalytic efficiency. The enhanced activities with γH2A.X-nucleosome coincide with increased accessibility of the DNA termini resulting from the H2A.X-Ser139 phosphorylation. Indeed, H2A- and (γ)H2A.X-nucleosomes have distinct stability characteristics, which are rationalized by mutational analysis and (γ)H2A.X-nucleosome core crystal structures. This suggests that the γH2A.X epigenetic marker directly facilitates DNA repair by stabilizing PARP1 association and promoting catalysis.


    Organizational Affiliation

    NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore. davey@ntu.edu.sg.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1A, E98Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B82Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC, G107Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
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Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD, H95Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
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Find proteins for P06899 (Homo sapiens)
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PHAROS:  P06899
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4F87Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)I145Homo sapiens
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (145-MER)J145Homo sapiens
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.56α = 90
b = 109.71β = 90
c = 183.48γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release