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


This is version 1.1 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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
139Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
106Homo 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
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UniProt GroupP62805
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AX
C, G
146Homo sapiensMutation(s): 0 
Gene Names: H2AFXH2AX
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
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
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
MoleculeChains LengthOrganismImage
DNA (145-MER)145Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-MER)145Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
L [auth D]
N [auth I]
O [auth I]
P [auth I]
Q [auth I]
L [auth D],
N [auth I],
O [auth I],
P [auth I],
Q [auth I],
R [auth I],
S [auth J],
T [auth J],
U [auth J],
V [auth J],
W [auth J],
X [auth J]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth C],
M [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description