6USJ

Structure of two nucleosomes bridged by human PARP2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1.

Gaullier, G.Roberts, G.Muthurajan, U.M.Bowerman, S.Rudolph, J.Mahadevan, J.Jha, A.Rae, P.S.Luger, K.

(2020) PLoS One 15: e0240932-e0240932

  • DOI: https://doi.org/10.1371/journal.pone.0240932
  • Primary Citation of Related Structures:  
    6USJ

  • PubMed Abstract: 

    Poly(ADP-ribose) Polymerase 2 (PARP2) is one of three DNA-dependent PARPs involved in the detection of DNA damage. Upon binding to DNA double-strand breaks, PARP2 uses nicotinamide adenine dinucleotide to synthesize poly(ADP-ribose) (PAR) onto itself and other proteins, including histones. PAR chains in turn promote the DNA damage response by recruiting downstream repair factors. These early steps of DNA damage signaling are relevant for understanding how genome integrity is maintained and how their failure leads to genome instability or cancer. There is no structural information on DNA double-strand break detection in the context of chromatin. Here we present a cryo-EM structure of two nucleosomes bridged by human PARP2 and confirm that PARP2 bridges DNA ends in the context of nucleosomes bearing short linker DNA. We demonstrate that the conformation of PARP2 bound to damaged chromatin provides a binding platform for the regulatory protein Histone PARylation Factor 1 (HPF1), and that the resulting HPF1•PARP2•nucleosome complex is enzymatically active. Our results contribute to a structural view of the early steps of the DNA damage response in chromatin.


  • Organizational Affiliation

    Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, United States of America.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1C [auth A],
G [auth E],
M [auth K],
Q [auth O]
139Homo sapiensMutation(s): 0 
Gene Names: 
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PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F],
N [auth L],
R [auth P]
106Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G],
O [auth M],
S [auth Q]
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABHIST1H2AEhCG_1640984hCG_1787383
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PHAROS:  P04908
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-JF [auth D],
J [auth H],
P [auth N],
T [auth R]
129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
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GTEx:  ENSG00000124635 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 2
U, V
590Homo sapiensMutation(s): 2 
Gene Names: PARP2ADPRT2ADPRTL2
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
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PHAROS:  Q9UGN5
GTEx:  ENSG00000129484 
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Entity ID: 1
MoleculeChains LengthOrganismImage
Widom 601 DNA (160-MER)A [auth I],
K [auth S]
165synthetic construct
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Entity ID: 2
MoleculeChains LengthOrganismImage
Widom 601 DNA (160-MER)B [auth J],
L [auth T]
165synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17-3644
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA218255

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references