6K1J

Human nucleosome core particle with H2A.X variant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 

wwPDB Validation   3D Report Full Report


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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:  
    6IPU, 6JXD, 6K1I, 6K1J, 6K1K

  • 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, E139Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
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Go to UniProtKB:  P68431
PHAROS:  P68431
GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775 
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UniProt GroupP68431
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F106Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126 
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UniProt GroupP62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AXC, G146Homo sapiensMutation(s): 0 
Gene Names: H2AFX, H2AX
UniProt & NIH Common Fund Data Resources
Find proteins for P16104 (Homo sapiens)
Explore P16104 
Go to UniProtKB:  P16104
PHAROS:  P16104
GTEx:  ENSG00000188486 
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UniProt GroupP16104
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD, H129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ, H2BFR, H2BC11
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
PHAROS:  P06899
GTEx:  ENSG00000124635 
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UniProt GroupP06899
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)I 145Homo sapiens
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)J 145Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.75α = 90
b = 109.94β = 90
c = 180.37γ = 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
Ministry of Education (Singapore)Singapore--

Revision History  (Full details and data files)

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