These authors contributed equally: Cai-Rong Sun, Da Xu, Fengrui Yang.

School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China

Cai-Rong Sun, Da Xu, Yuxing Chen, Qiong Li & Cong-Zhao Zhou

Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China

Cai-Rong Sun, Da Xu, Yuxing Chen, Qiong Li & Cong-Zhao Zhou

MOE Key Laboratory for Cellular Dynamics, University of Science and Technology of China, Hefei, Anhui, China

Fengrui Yang & Xuebiao Yao

School of Chemistry and Materials Science, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, China

Zhuanghao Hou & Guangming Huang

Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, China

Yuyao Luo & Ge Shan

Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China

Chen-Yu Zhang

C.Z.Z., Y.C. and Q.L. conceptualized and supervised the project. C.R.S., D.X. and Q.L. designed all the experiments. C.Y.Z. provides the plasmid encoding SIDT1. C.R.S. performed cloning, expression, purification and cryo-EM sample preparation. C.R.S. and D.X. preformed cryo-EM data collection, structure determination and model refinement. C.R.S. preformed phospholipase activity assays. Z.H. and G.H. performed mass spectrometry analyses. F.Y., X.Y., Y.L. and G.S. performed fluorescence experiments and data analyses. Q.L., C.R.S., C.Z.Z. and Y.C. wrote the manuscript.

Correspondence to Xuebiao Yao, Yuxing Chen, Qiong Li or Cong-Zhao Zhou.