6M3I

Crystal structure of HPF1/PARP1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones.

Sun, F.H.Zhao, P.Zhang, N.Kong, L.L.Wong, C.C.L.Yun, C.H.

(2021) Nat Commun 12: 1028-1028

  • DOI: https://doi.org/10.1038/s41467-021-21302-4
  • Primary Citation of Related Structures:  
    6M3G, 6M3H, 6M3I

  • PubMed Abstract: 

    Upon binding to DNA breaks, poly(ADP-ribose) polymerase 1 (PARP1) ADP-ribosylates itself and other factors to initiate DNA repair. Serine is the major residue for ADP-ribosylation upon DNA damage, which strictly depends on HPF1. Here, we report the crystal structures of human HPF1/PARP1-CAT ΔHD complex at 1.98 Å resolution, and mouse and human HPF1 at 1.71 Å and 1.57 Å resolution, respectively. Our structures and mutagenesis data confirm that the structural insights obtained in a recent HPF1/PARP2 study by Suskiewicz et al. apply to PARP1. Moreover, we quantitatively characterize the key residues necessary for HPF1/PARP1 binding. Our data show that through salt-bridging to Glu284/Asp286, Arg239 positions Glu284 to catalyze serine ADP-ribosylation, maintains the local conformation of HPF1 to limit PARP1 automodification, and facilitates HPF1/PARP1 binding by neutralizing the negative charge of Glu284. These findings, along with the high-resolution structural data, may facilitate drug discovery targeting PARP1.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Peking University Health Science Center, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone PARylation factor 1346Homo sapiensMutation(s): 0 
Gene Names: HPF1C4orf27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWY4 (Homo sapiens)
Go to UniProtKB:  Q9NWY4
PHAROS:  Q9NWY4
GTEx:  ENSG00000056050 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1253Homo sapiensMutation(s): 0 
Gene Names: PARP1ADPRTPPOL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens)
Go to UniProtKB:  P09874
PHAROS:  P09874
GTEx:  ENSG00000143799 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UNU (Subject of Investigation/LOI)
Query on UNU

Download Ideal Coordinates CCD File 
C [auth B]BENZAMIDE
C7 H7 N O
KXDAEFPNCMNJSK-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UNU BindingDB:  6M3I IC50: min: 5400, max: 2.20e+4 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.858α = 90
b = 84.179β = 107.49
c = 81.731γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31270769

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description