7LH9

Crystal structure of BRPF2 PWWP domain in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the BRPF2 PWWP domain in complex with DNA reveals a different binding mode than the HDGF family of PWWP domains.

Zhang, M.Lei, M.Qin, S.Dong, A.Yang, A.Li, Y.Loppnau, P.Hughes, T.R.Min, J.Liu, Y.

(2021) Biochim Biophys Acta Gene Regul Mech 1864: 194688-194688

  • DOI: https://doi.org/10.1016/j.bbagrm.2021.194688
  • Primary Citation of Related Structures:  
    7LH9

  • PubMed Abstract: 

    The PWWP domain was first identified in the HDGF protein family and named after the conserved Proline-Tryptophan-Tryptophan-Proline motif in WHSC1. The PWWP domain-containing proteins play important roles in different biological processes, such as DNA replication, transcription, DNA repair, pre-mRNA processing by recognizing methylated histone and dsDNA simultaneously. Recently, how the HDGF family of PWWP domains recognize histone H3K36me3-modified nucleosome has been reported. In order to better understand the interactions between the PWWP domain and dsDNA, we carried out family-wide characterization of dsDNA binding abilities of human PWWP domains. Our binding assays confirmed that PWWP domains bind to dsDNA without sequence selectivity. Our crystal structure of the BRPF2 PWWP domain in complex with a 12-mer dsDNA reveals that the PWWP domain interacts with dsDNA by binding to its major groove, instead of the minor groove observed in the HDGF family of PWWP domains. Our study indicates that PWWP domains could bind to dsDNA in different modes.


  • Organizational Affiliation

    College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 1
A, B, C, D
126Homo sapiensMutation(s): 0 
Gene Names: BRD1BRLBRPF2
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens)
Explore O95696 
Go to UniProtKB:  O95696
PHAROS:  O95696
GTEx:  ENSG00000100425 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95696
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA
E, F, G, H, I
E, F, G, H, I, J, K, L
12synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.41α = 90
b = 216.113β = 109.42
c = 54.037γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description