R6

Khanppnavar, B.*, North, R. A.*, Ventura, S.*, and Xu, Y.* (2024) Advances, challenges, and opportunities in structural biology. Trends Biochem Sci

R5

Chen, X., and Xu, Y.* (2024) Interplay between the transcription preinitiation complex and the +1 nucleosome. Trends Biochem Sci

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

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

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

41

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

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

R3

Chen, X., and Xu, Y.* (2022) Structural insights into assembly of transcription preinitiation complex. Curr Opin Struct Biol 75, 102404

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

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

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

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

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

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

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

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

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

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

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

27

Feng, Y., Tian, Y., Wu, Z., and Xu, Y.* (2018) Cryo-EM structure of human SRCAP complex. Cell Res 28, 1121-1123

R2

Yang H*, Chen X, Liu M, Xu, Y.* (2018) The structure of mTOR complexes at a glance. Precis Cancer Med 1:7 (review)

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

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

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]

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

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

R1

Yin, X., and Xu, Y.* (2016). Structure and Function of TET Enzymes. Adv Exp Med Biol 945, 275-302. (Book Chapter)

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

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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]

Highlights: Features of the PHF8/KIAA1718 histone demethylase. Cell research 20(8):861-2.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.