Structured low-rank (SLR) algorithms are emerging as powerful image reconstruction approaches because they can capitalize on several signal properties, which conventional image-based approaches have difficulty in exploiting. The main challenge with this scheme that self learns an annihilation convolutional filterbank from the undersampled data is its high computational complexity. We introduce a deep-learning approach to quite significantly reduce the computational complexity of SLR schemes. Specifically, we pre-learn a CNN-based annihilation filterbank from exemplar data, which is used as a prior in a model-based reconstruction scheme. The CNN parameters are learned in an end-to-end fashion by un-rolling the iterative algorithm. The main difference of the proposed scheme with current model-based deep learning strategies is the learning of non-linear annihilation relations in Fourier space using a modelbased framework. The experimental comparisons show that the proposed scheme can offer similar performance as SLR schemes in the calibrationless parallel MRI setting, while reducing the run-time by around three orders of magnitude. We also combine the proposed scheme with image domain priors, which are complementary, thus further improving the performance over SLR schemes.