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The Arabidopsis WRKY11 (AtWRKY11) protein is an important transcription factor involved in plant response to biotic and abiotic stresses. Its DNA-binding domain specifically binds to gene promoter regions harboring the W-box consensus motif. Herein we report the high-resolution structure of the AtWRKY11 DNA-binding domain (DBD) determined by solution NMR spectroscopy. The results show that AtWRKY11-DBD adopts an all-β fold comprising five β-strands packed in an antiparallel topology, stabilized by a zinc-finger motif. Structural comparison reveals that the long β 1 -β 2 loop shows the highest structural variation from other available WRKY domain structures. Moreover, this loop was further found to contribute to the binding between AtWRKY11-DBD and W-box DNA. Our current study provides atomic-level structural basis for further understanding the structure-function relationship of plant WRKY proteins. • This is the first structure reported for the IId subgroup of the WRKY superfamily. • The β1-β2 loop region of AtWRKY11-DBD shows high variation among other WRKY proteins. • The DNA-binding site on AtWRKY11 involves not only the consensus WRKY motif, but also the aforementioned β1-β2 loop region. • Our model of the AtWRKY11-DNA complex suggests the possible roles of the β1-β2 loop in binding DNA. [ABSTRACT FROM AUTHOR]