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: 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 ...

    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
MoleculeChainsSequence 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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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
GTEx:  ENSG00000197409ENSG00000197153ENSG00000278828ENSG00000275714ENSG00000273983ENSG00000274750ENSG00000275379ENSG00000277775
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D [auth B], H [auth F], N [auth L], R [auth P]106Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
GTEx:  ENSG00000274618ENSG00000197238ENSG00000197837ENSG00000158406ENSG00000278705ENSG00000197061ENSG00000270882ENSG00000270276ENSG00000273542ENSG00000277157ENSG00000276966ENSG00000276180ENSG00000278637ENSG00000275126
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AE [auth C], I [auth G], O [auth M], S [auth Q]133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AB, HIST1H2AE, hCG_1640984, hCG_1787383, H2AC4, H2AFM, H2AC8, H2AFA
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Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
GTEx:  ENSG00000277075ENSG00000278463
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JF [auth D], J [auth H], P [auth N], T [auth R]129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ, H2BFR, H2BC11
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Find proteins for P06899 (Homo sapiens)
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PHAROS:  P06899
GTEx:  ENSG00000124635
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 2U, V590Homo sapiensMutation(s): 2 
Gene Names: PARP2, ADPRT2, ADPRTL2
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
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GTEx:  ENSG00000129484
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Widom 601 DNA (160-MER)A [auth I], K [auth S]165synthetic construct
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Entity ID: 2
MoleculeChainsLengthOrganismImage
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 

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