4RXJ

crystal structure of WHSC1L1-PWWP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Histone and DNA binding ability studies of the NSD subfamily of PWWP domains.

Zhang, M.Yang, Y.Zhou, M.Dong, A.Yan, X.Loppnau, P.Min, J.Liu, Y.

(2021) Biochem Biophys Res Commun 569: 199-206

  • DOI: 10.1016/j.bbrc.2021.07.017
  • Primary Citation of Related Structures:  
    4RXJ, 5VC8

  • PubMed Abstract: 
  • The NSD proteins, namely NSD1, NSD2 and NSD3, are lysine methyltransferases, which catalyze mono- and di-methylation of histone H3K36. They are multi-domain proteins, including two PWWP domains (PWWP1 and PWWP2) separated by some other domains. These proteins act as potent oncoproteins and are implicated in various cancers ...

    The NSD proteins, namely NSD1, NSD2 and NSD3, are lysine methyltransferases, which catalyze mono- and di-methylation of histone H3K36. They are multi-domain proteins, including two PWWP domains (PWWP1 and PWWP2) separated by some other domains. These proteins act as potent oncoproteins and are implicated in various cancers. However the biological functions of these PWWP domains are still largely unknown. To better understand the functions of these proteins' PWWP domains, we cloned, expressed and purified all the PWWP domains of these NSD proteins to characterize their interactions with methylated histone peptides and dsDNA by quantitative binding assays and crystallographic analysis. Our studies indicate that all these PWWP domains except NSD1_PWWP1 bind to trimethylated H3K36, H3K79 peptides and dsDNA weakly. Our crystal structures uncover that the NDS3_PWWP2 and NSD2_PWWP1 domains, which hold an extremely long α-helix and α-helix bundle, respectively, need a conformation adjustment to interact with nucleosome.


    Organizational Affiliation

    College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China. Electronic address: ylliu18@suda.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase NSD3A113Homo sapiensMutation(s): 0 
Gene Names: WHSC1L1NSD3DC28
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.370 (UniProt), 2.1.1.371 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZ95 (Homo sapiens)
Explore Q9BZ95 
Go to UniProtKB:  Q9BZ95
PHAROS:  Q9BZ95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZ95
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.357α = 90
b = 99.476β = 90
c = 41.552γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Data collection, Database references