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In this paper we introduce StructNet-CE, a novel real-time online learning framework for MIMO-OFDM channel estimation, which only utilizes over-the-air (OTA) pilot symbols for online training and converges within one OFDM subframe. The design of StructNet-CE leverages the structure information in the MIMO-OFDM system, including the repetitive structure of modulation constellation and the invariant property of symbol classification to inter-stream interference. The embedded structure information enables StructNet-CE to conduct channel estimation with a binary classification task and accurately learn channel coefficients with as few as two pilot OFDM symbols. Experiments show that the channel estimation performance is significantly improved with the incorporation of structure knowledge. StructNet-CE is compatible and readily applicable to current and future wireless networks, demonstrating the effectiveness and importance of combining machine learning techniques with domain knowledge for wireless communication systems.