Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds.

Qiu, C.Sawada, K.Zhang, X.Cheng, X.

(2002) Nat Struct Biol 9: 217-224

  • DOI: https://doi.org/10.1038/nsb759
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The PWWP domain is a weakly conserved sequence motif found in > 60 eukaryotic proteins, including the mammalian DNA methyltransferases Dnmt3a and Dnmt3b. These proteins often contain other chromatin-association domains. A 135-residue PWWP domain from mouse Dnmt3b (amino acids 223--357) has been structurally characterized at 1.8 A resolution. The N-terminal half of this domain resembles a barrel-like five-stranded structure, whereas the C-terminal half contains a five-helix bundle. The two halves are packed against each other to form a single structural module that exhibits a prominent positive electrostatic potential. The PWWP domain alone binds DNA in vitro, probably through its basic surface. We also show that recombinant Dnmt3b2 protein (a splice variant of Dnmt3b) and two N-terminal deletion mutants (Delta218 and Delta369) have approximately equal methyl transfer activity on unmethylated and hemimethylated CpG-containing oligonucleotides. The Delta218 protein, which includes the PWWP domain, binds DNA more strongly than Delta369, which lacks the PWWP domain.

  • Organizational Affiliation

    Department of Biochemistry, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA cytosine-5 methyltransferase 3B2147Mus musculusMutation(s): 0 
Gene Names: Dnmt3b
UniProt & NIH Common Fund Data Resources
Find proteins for O88509 (Mus musculus)
Explore O88509 
Go to UniProtKB:  O88509
IMPC:  MGI:1261819
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88509
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on UNX

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.75α = 90
b = 52.75β = 90
c = 186.86γ = 120
Software Package:
Software NamePurpose
RESOLVEmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations