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Selected publications (corresponding author)
~2004 ~2008 2010 2011 2012 2013 2014 2015 2016 2017
2018 2019 2020 2021 2022 2023 2024      

  2024  
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

  2023  
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
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)
Link
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

  2022  
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
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

  2021  
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

  2020  
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

  2019  
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

  2018  
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]

  2017  
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

  2016  
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

 
2015
 
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
   

 
2014
 
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

 
2013
 
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

  2012  
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

  2011  
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

  2010  
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.

  2004-2008 (first author)
At Princeton University (As a Postodoctoral Fellow)
 
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.
 

  1999-2004 (first author)
At Tsinghua University (As a Graduate Student)
 
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.
 

The Lab of Structural Biology, Shanghai Cancer Center/Institutes of Biomedical Sciences, Fudan University