Cryo-EM structures of human m6A writer complexes

Shichen Su; Shanshan Li; Ting Deng; Minsong Gao; Yue Yin; Baixing Wu; Chao Peng; Jianzhao Liu; Jinbiao Ma; Kaiming Zhang

doi:10.1038/s41422-022-00725-8

Cryo-EM structures of human m⁶A writer complexes

Cell Res. 2022 Nov;32(11):982-994. doi: 10.1038/s41422-022-00725-8. Epub 2022 Sep 27.

Authors

Shichen Su^#¹, Shanshan Li^#², Ting Deng^#¹, Minsong Gao³, Yue Yin⁴, Baixing Wu^{1

5}, Chao Peng⁴, Jianzhao Liu³, Jinbiao Ma⁶, Kaiming Zhang⁷

Affiliations

¹ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China.
² MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
³ MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, China.
⁴ National Facility for Protein Science in Shanghai, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China.
⁵ Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
⁶ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China. majb@fudan.edu.cn.
⁷ MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. kmzhang@ustc.edu.cn.

^# Contributed equally.

Abstract

N⁶-methyladenosine (m⁶A) is the most abundant ribonucleotide modification among eukaryotic messenger RNAs. The m⁶A "writer" consists of the catalytic subunit m⁶A-METTL complex (MAC) and the regulatory subunit m⁶A-METTL-associated complex (MACOM), the latter being essential for enzymatic activity. Here, we report the cryo-electron microscopy (cryo-EM) structures of MACOM at a 3.0-Å resolution, uncovering that WTAP and VIRMA form the core structure of MACOM and that ZC3H13 stretches the conformation by binding VIRMA. Furthermore, the 4.4-Å resolution cryo-EM map of the MACOM-MAC complex, combined with crosslinking mass spectrometry and GST pull-down analysis, elucidates a plausible model of the m⁶A writer complex, in which MACOM binds to MAC mainly through WTAP and METTL3 interactions. In combination with in vitro RNA substrate binding and m⁶A methyltransferase activity assays, our results illustrate the molecular basis of how MACOM assembles and interacts with MAC to form an active m⁶A writer complex.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cryoelectron Microscopy
Humans
Methyltransferases* / metabolism
RNA, Messenger / metabolism

Substances

RNA, Messenger
METTL3 protein, human
Methyltransferases