Selected publications (corresponding author)
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2024 |
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R6 |
Khanppnavar, B.*, North, R. A.*, Ventura, S.*, and Xu, Y.* (2024) Advances, challenges, and opportunities in structural biology. Trends Biochem Sci |
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R5 |
Chen, X., and Xu, Y.* (2024) Interplay between the transcription preinitiation complex and the +1 nucleosome. Trends Biochem Sci |
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2023 |
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44 |
Chen, X., Liu, W., Wang, Q., Wang, X., Ren, Y., Qu, X., Li, W., and Xu, Y.* (2023) Structural visualization of transcription initiation in action. Science 382, eadi5120 |
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R4 |
Fass, D.*, and Xu, Y.*(2023) Macromolecular assemblies: Molecular mechanisms abound. Curr Opin Struct Biol 81, 102639
Yanhui Xu is a guest editor of the special issue: Macromolecular Assemblies (2023) |
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43 |
Hou, H., Jin, Q., Ren, Y., Chen, Z., Wang, Q.*, and Xu, Y.* (2023) Structure of the SNAPc-bound RNA polymerase III preinitiation complex. Cell Res |
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42 |
Zheng, H., Jin, Q., Wang, X., Qi, Y., Liu, W., Ren, Y., Zhao, D., Xavier Chen, F., Cheng, J., Chen, X., and Xu, Y.* (2023) Structural basis of INTAC-regulated transcription. Protein Cell |
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2022 |
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41 |
Wang, L., Yu, J., Yu, Z., Wang, Q., Li, W., Ren, Y., Chen, Z., He, S., and Xu, Y.* (2022) Structure of nucleosome-bound human PBAF complex. Nat Commun 13, 7644 |
Link |
40 |
Chen, X., Wang, X., Liu, W., Ren, Y., Qu, X., Li, J., Yin, X., and Xu, Y.* (2022) Structures of +1 nucleosome-bound PIC-Mediator complex. Science 378, 62-68 |
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39 |
Wang, X., Qi, Y., Wang, Z., Wang, L., Song, A., Tao, B., Li, J., Zhao, D., Zhang, H., Jin, Q., Jiang, Y. Z., Chen, F. X.*, Xu, Y.*, and Chen, X.* (2022) RPAP2 regulates a transcription initiation checkpoint by inhibiting assembly of pre-initiation complex. Cell Rep 39, 110732 |
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R3 |
Chen, X., and Xu, Y.* (2022) Structural insights into assembly of transcription preinitiation complex. Curr Opin Struct Biol 75, 102404 |
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2021 |
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38 |
Hou, H., Li, Y., Wang, M., Liu, A., Yu, Z., Chen, K., Zhao, D., and Xu, Y.* (2021) Structural insights into RNA polymerase III-mediated transcription termination through trapping poly-deoxythymidine. Nat Commun 12, 6135 |
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37 |
Zhao, D., Liu, W., Chen, K., Wu, Z., Yang, H., and Xu, Y.* (2021) Structure of the human RNA polymerase I elongation complex. Cell Discov 7, 97 |
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36 |
Chen, X., Yin, X., Li, J., Wu, Z., Qi, Y., Wang, X., Liu, W., and Xu, Y.* (2021) Structures of the human Mediator and Mediator-bound preinitiation complex. Science 372, eabg0635 |
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35 |
Chen, X., Qi, Y., Wu, Z., Wang, X., Li, J., Zhao, D., Hou, H., Li, Y., Yu, Z., Liu, W., Wang, M., Ren, Y., Li, Z., Yang, H., and Xu, Y.* (2021) Structural insights into preinitiation complex assembly on core promoters. Science 372, eaba8490 |
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34 |
Li, L., Yu, Z., Zhao, D., Ren, Y., Hou, H.*, and Xu, Y.* (2021) Structure of human RNA polymerase III elongation complex. Cell Res 31, 791-800 |
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33 |
Yang, H., Yu, Z., Chen, X., Li, J., Li, N., Cheng, J., Gao, N., Yuan, H. X., Ye, D., Guan, K. L., and Xu, Y.* (2021) Structural insights into TSC complex assembly and GAP activity on Rheb. Nat Commun 12, 339 |
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2020 |
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32 |
Zheng, H., Qi, Y., Hu, S., Cao, X., Xu, C., Yin, Z., Chen, X., Li, Y., Liu, W., Li, J., Wang, J., Wei, G., Liang, K., Chen, F. X.*, and Xu, Y.* (2020) Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase. Science 370, eabb5872 |
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31 |
He, S., Wu, Z., Tian, Y., Yu, Z., Yu, J., Wang, X., Li, J., Liu, B., and Xu, Y.* (2020) Structure of nucleosome-bound human BAF complex. Science 367, 875-881 |
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30 |
Pan, B., Yang, Y., Li, J., Wang, Y., Fang, C., Yu, F. X.*, and Xu, Y.* (2020) USP47-mediated deubiquitination and stabilization of YAP contributes to the progression of colorectal cancer. Protein Cell 11, 138-143 |
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2019 |
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29 |
Zhu, L., Li, L., Qi, Y., Yu, Z., and Xu, Y.* (2019) Cryo-EM structure of SMG1-SMG8-SMG9 complex. Cell Res 29, 1027-1034 |
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28 |
Xiao, J., Liu, M., Qi, Y., Chaban, Y., Gao, C., Pan, B., Tian, Y., Yu, Z., Li, J., Zhang, P., and Xu, Y.* (2019) Structural insights into the activation of ATM kinase. Cell Res 29, 683-685 |
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2018 |
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27 |
Feng, Y., Tian, Y., Wu, Z., and Xu, Y.* (2018) Cryo-EM structure of human SRCAP complex. Cell Res 28, 1121-1123 |
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R2 |
Yang H*, Chen X, Liu M, Xu, Y.* (2018) The structure of mTOR complexes at a glance. Precis Cancer Med 1:7 (review) |
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26 |
Chen, X., Liu, M., Tian, Y., Li, J., Qi, Y., Zhao, D., Wu, Z., Huang, M., Wong, C. C. L., Wang, H. W., Wang, J., Yang, H.*, and Xu, Y.* (2018) Cryo-EM structure of human mTOR complex 2. Cell Res 28, 518-528 |
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25 |
Rao, Q., Liu, M., Tian, Y., Wu, Z., Hao, Y., Song, L., Qin, Z., Ding, C., Wang, H. W.*, Wang, J.*, and Xu, Y.* (2018) Cryo-EM structure of human ATR-ATRIP complex. Cell Res 28, 143-156 |
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24 |
He, X. D., Gong, W., Zhang, J. N., Nie, J., Yao, C. F., Guo, F. S., Lin, Y., Wu, X. H., Li, F., Li, J., Sun, W. C., Wang, E. D., An, Y. P., Tang, H. R., Yan, G. Q., Yang, P. Y., Wei, Y., Mao, Y. Z., Lin, P. C., Zhao, J. Y., Xu, Y.*, Xu, W.*, and Zhao, S. M.* (2018) Sensing and Transmitting Intracellular Amino Acid Signals through Reversible Lysine Aminoacylations. Cell Metab 27, 151-166 e156 [ Cover Story] |
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2017 |
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23 |
Yin, X., Liu, M., Tian, Y., Wang, J., and Xu, Y.* (2017) Cryo-EM structure of human DNA-PK holoenzyme. Cell Res 27, 1341-1350 |
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2016 |
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22 |
Yang, H., Wang, J., Liu, M., Chen, X., Huang, M., Tan, D., Dong, M. Q., Wong, C. C., Wang, J., Xu, Y.*, and Wang, H. W.* (2016) 4.4 A Resolution Cryo-EM structure of human mTOR Complex 1. Protein Cell 7, 878-887 |
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R1 |
Yin, X., and Xu, Y.* (2016). Structure and Function of TET Enzymes. Adv Exp Med Biol 945, 275-302. (Book Chapter) |
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21 |
Fang, J., Cheng, J., Wang, J., Zhang, Q., Liu, M., Gong, R., Wang, P., Zhang, X., Feng, Y., Lan, W., Gong, Z., Tang, C., Wong, J., Yang, H., Cao, C., and Xu, Y.* (2016) Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition. Nat Commun 7, 11197 |
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20 |
Hu, L., Lu, J., Cheng, J., Rao, Q., Li, Z., Hou, H., Lou, Z., Zhang, L., Li, W., Gong, W., Liu, M., Sun, C., Yin, X., Li, J., Tan, X., Wang, P., Wang, Y., Fang, D., Cui, Q., Yang, P., He, C., Jiang, H., Luo, C.*, and Xu, Y.* (2015) Structural insight into substrate preference for TET-mediated oxidation. Nature 527, 118-122 |
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19 |
Cheng, J., Li, Z., Gong, R., Fang, J., Yang, Y., Sun, C., Yang, H., and Xu, Y.* (2015) Molecular mechanism for the substrate recognition of USP7. Protein Cell 6, 849-852 |
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18 |
Gong, R., Hong, A. W., Plouffe, S. W., Zhao, B., Liu, G., Yu, F. X.*, Xu, Y.*, and Guan, K. L.* (2015) Opposing roles of conventional and novel PKC isoforms in Hippo-YAP pathway regulation. Cell Res 25, 985-988 |
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17 |
Cheng, J., Yang, H., Fang, J., Ma, L., Gong, R., Wang, P., Li, Z., and Xu, Y.* (2015) Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation. Nat Commun 6, 7023 |
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16 |
Wang, P., Sun, C., Zhu, T., and Xu, Y.* (2015) Structural insight into mechanisms for dynamic regulation of PKM2. Protein Cell 6, 275-287 (Cover story)
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15 |
Yang, Y., Yin, X., Yang, H., and Xu, Y.* (2015) Histone demethylase LSD2 acts as an E3 ubiquitin ligase and inhibits cancer cell growth through promoting proteasomal degradation of OGT. Mol Cell 58, 47-59
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14 |
Guo, X., Wang, L., Li, J., Ding, Z., Xiao, J., Yin, X., He, S., Shi, P., Dong, L., Li, G., Tian, C., Wang, J., Cong, Y., and Xu, Y.* (2015) Structural insight into autoinhibition and histone H3-induced activation of DNMT3A. Nature 517, 640-644
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13 |
Zhu, T., Roundtree, I. A., Wang, P., Wang, X., Wang, L., Sun, C., Tian, Y., Li, J., He, C., and Xu, Y.* (2014) Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine. Cell Res 24, 1493-1496
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12 |
Zhang, Y., Yang, H., Guo, X., Rong, N., Song, Y., Xu, Y., Lan, W., Zhang, X., Liu, M., Xu, Y.*, and Cao, C.* (2014) The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B. Protein Cell 5, 837-850
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11 |
Hu, L., Li, Z., Cheng, J., Rao, Q., Gong, W., Liu, M., Shi, Y. G., Zhu, J., Wang, P., and Xu, Y.* (2013) Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation. Cell 155, 1545-1555 |
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10 |
Fang, R., Chen, F., Dong, Z., Hu, D., Barbera, A. J., Clark, E. A., Fang, J., Yang, Y., Mei, P., Rutenberg, M., Li, Z., Zhang, Y., Xu, Y., Yang, H., Wang, P., Simon, M. D., Zhou, Q., Li, J., Marynick, M. P., Li, X., Lu, H., Kaiser, U. B., Kingston, R. E., Xu, Y.*, and Shi, Y. G.* (2013) LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol Cell 49, 558-570
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9 |
Cheng, J., Yang, Y., Fang, J., Xiao, J., Zhu, T., Chen, F., Wang, P., Li, Z., Yang, H., and Xu, Y.* (2013) Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein. J Biol Chem 288, 1329-1339 |
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8 |
Chen, F., Yang, H., Dong, Z., Fang, J., Wang, P., Zhu, T., Gong, W., Fang, R., Shi, Y. G., Li, Z.*, and Xu, Y.* (2013) Structural insight into substrate recognition by histone demethylase LSD2/KDM1b. Cell Res 23, 306-309 |
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2012 |
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7 |
Ma, H., Chen, H., Guo, X., Wang, Z., Sowa, M. E., Zheng, L., Hu, S., Zeng, P., Guo, R., Diao, J., Lan, F., Harper, J. W., Shi, Y. G., Xu, Y.*, and Shi, Y.* (2012) M phase phosphorylation of the epigenetic regulator UHRF1 regulates its physical association with the deubiquitylase USP7 and stability. Proc Natl Acad Sci U S A 109, 4828-4833 |
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2011 |
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6 |
Gong, R., Li, L., Liu, Y., Wang, P., Yang, H., Wang, L., Cheng, J., Guan, K. L.*, and Xu, Y.* (2011) Crystal structure of the Gtr1p-Gtr2p complex reveals new insights into the amino acid-induced TORC1 activation. Genes Dev 25, 1668-1673 |
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5 |
Hu, L., Li, Z., Wang, P., Lin, Y., and Xu, Y.* (2011) Crystal structure of PHD domain of UHRF1 and insights into recognition of unmodified histone H3 arginine residue 2. Cell Res 21, 1374-1378 |
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4 |
Jeong, B. R., Lin, Y., Joe, A., Guo, M., Korneli, C., Yang, H., Wang, P., Yu, M., Cerny, R. L., Staiger, D., Alfano, J. R.*, and Xu, Y.* (2011) Structure function analysis of an ADP-ribosyltransferase type III effector and its RNA-binding target in plant immunity. J Biol Chem 286, 43272-43281 |
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2010 |
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3 |
Li, Z., Zhao, B., Wang, P., Chen, F., Dong, Z., Yang, H., Guan, K. L.*, and Xu, Y.* (2010) Structural insights into the YAP and TEAD complex. Genes Dev 24, 235-240 |
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2 |
Lin, H., Wang, Y., Wang, Y., Tian, F., Pu, P., Yu, Y., Mao, H., Yang, Y., Wang, P., Hu, L., Lin, Y., Liu, Y., Xu, Y.*, and Chen, C. D.* (2010) Coordinated regulation of active and repressive histone methylations by a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans. Cell Res 20, 899-907 |
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1 |
Yang, Y., Hu, L., Wang, P., Hou, H., Lin, Y., Liu, Y., Li, Z., Gong, R., Feng, X., Zhou, L., Zhang, W., Dong, Y., Yang, H., Lin, H., Wang, Y., Chen, C. D.*, and Xu, Y.* (2010) Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans. Cell Res 20, 886-898 [ Cover story]
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2004-2008 (first author)
At Princeton University (As a Postodoctoral Fellow) |
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12 |
Xu, Y. #, Xing, Y. #, Chen, Y. #, Chao, Y. #, Lin, Z., Fan, E., Yu, J.W., Strack, S., Jeffrey, P.D. and Shi, Y. (2006) Structure of the protein phosphatase 2A holoenzyme. Cell 127, 1239-1251. |
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11 |
Xing, Y. #, Xu, Y. #, Chen, Y. #, Jeffrey, P.D., Chao, Y., Lin, Z., Li, Z., Strack, S., Stock, J.B. and Shi, Y. (2006) Structure of protein phosphatase 2A core enzyme bound to tumor-inducing toxins. Cell 127, 341-353. |
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10 |
Xu, Y. #, Chen, Y. #, Zhang, P., Jeffrey, P.D. and Shi, Y. (2008) Structure of a protein phosphatase 2A holoenzyme: insights into B55-mediated Tau dephosphorylation. Molecular cell 31, 873-885. |
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9 |
Chen, Y. #, Xu, Y. #, Bao, Q., Xing, Y., Li, Z., Lin, Z., Stock, J.B., Jeffrey, P.D. and Shi, Y. (2007) Structural and biochemical insights into the regulation of protein phosphatase 2A by small t antigen of SV40. Nature structural & molecular biology 14, 527-534. |
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1999-2004 (first author)
At Tsinghua University (As a Graduate Student) |
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8 |
Xu, Y., Lou, Z., Liu, Y., Pang, H., Tien, P., Gao, G.F. and Rao, Z. (2004) Crystal structure of severe acute respiratory syndrome coronavirus spike protein fusion core. The Journal of biological chemistry 279, 49414-49419. |
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7 |
Xu, Y. #, Liu, Y. #, Lou, Z. #, Qin, L., Li, X., Bai, Z., Pang, H., Tien, P., Gao, G.F. and Rao, Z. (2004) Structural basis for coronavirus-mediated membrane fusion. Crystal structure of mouse hepatitis virus spike protein fusion core. The Journal of biological chemistry 279, 30514-30522. |
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6 |
Xu, Y., Zhu, J., Liu, Y., Lou, Z., Yuan, F., Liu, Y., Cole, D.K., Ni, L., Su, N., Qin, L., Li, X., Bai, Z., Bell, J.I., Pang, H., Tien, P., Gao, G.F. and Rao, Z. (2004) Characterization of the heptad repeat regions, HR1 and HR2, and design of a fusion core structure model of the spike protein from severe acute respiratory syndrome (SARS) coronavirus. Biochemistry 43, 14064-14071. |
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5 |
Xu, Y., Gao, S., Cole, D.K., Zhu, J., Su, N., Wang, H., Gao, G.F. and Rao, Z. (2004) Basis for fusion inhibition by peptides: analysis of the heptad repeat regions of the fusion proteins from Nipah and Hendra viruses, newly emergent zoonotic paramyxoviruses. Biochemical and biophysical research communications 315, 664-670. |
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4 |
Xu, Y., Cole, D.K., Lou, Z., Liu, Y., Qin, L., Li, X., Bai, Z., Yuan, F., Rao, Z. and Gao, G.F. (2004) Construct design, biophysical, and biochemical characterization of the fusion core from mouse hepatitis virus (a coronavirus) spike protein. Protein expression and purification 38, 116-122. |
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3 |
Xu, Y., Su, N., Qin, L., Bai, Z., Gao, G.F. and Rao, Z. (2004) Crystallization and preliminary crystallographic analysis of the heptad-repeat complex of SARS coronavirus spike protein. Acta Crystallogr Sect D 60, 2377-2379. |
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2 |
Xu, Y., Lou, Z., Liu, Y., Cole, D.K., Su, N., Qin, L., Li, X., Bai, Z., Rao, Z. and Gao, G.F. (2004) Crystallization and preliminary crystallographic analysis of the fusion core from two new zoonotic paramyxoviruses, Nipah virus and Hendra virus. Acta Crystallogr Sect D 60, 1161-1164. |
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1 |
Xu, Y., Bai, Z., Qin, L., Li, X., Gao, G. and Rao, Z. (2004) Crystallization and preliminary crystallographic analysis of the fusion core of the spike protein of the murine coronavirus mouse hepatitis virus (MHV). Acta Crystallogr Sect D 60, 2013-2015. |
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